diff --git a/src/freedreno/vulkan/tu_cmd_buffer.c b/src/freedreno/vulkan/tu_cmd_buffer.c
index 88d6a3d4b50..85bf1f509bb 100644
--- a/src/freedreno/vulkan/tu_cmd_buffer.c
+++ b/src/freedreno/vulkan/tu_cmd_buffer.c
@@ -1382,8 +1382,17 @@ tu6_render_tile(struct tu_cmd_buffer *cmd, struct tu_cs *cs,
 
    trace_start_draw_ib_gmem(&cmd->trace, &cmd->cs);
 
+   /* Primitives that passed all tests are still counted in in each
+    * tile even with HW binning beforehand. Do not permit it.
+    */
+   if (cmd->state.prim_generated_query_running_before_rp)
+      tu6_emit_event_write(cmd, cs, STOP_PRIMITIVE_CTRS);
+
    tu_cs_emit_call(cs, &cmd->draw_cs);
 
+   if (cmd->state.prim_generated_query_running_before_rp)
+      tu6_emit_event_write(cmd, cs, START_PRIMITIVE_CTRS);
+
    if (use_hw_binning(cmd)) {
       tu_cs_emit_pkt7(cs, CP_SET_MARKER, 1);
       tu_cs_emit(cs, A6XX_CP_SET_MARKER_0_MODE(RM6_ENDVIS));
@@ -1747,6 +1756,9 @@ tu_BeginCommandBuffer(VkCommandBuffer commandBuffer,
    } else if (cmd_buffer->vk.level == VK_COMMAND_BUFFER_LEVEL_SECONDARY) {
       assert(pBeginInfo->pInheritanceInfo);
 
+      cmd_buffer->inherited_pipeline_statistics =
+         pBeginInfo->pInheritanceInfo->pipelineStatistics;
+
       vk_foreach_struct(ext, pBeginInfo->pInheritanceInfo) {
          switch (ext->sType) {
          case VK_STRUCTURE_TYPE_COMMAND_BUFFER_INHERITANCE_CONDITIONAL_RENDERING_INFO_EXT: {
diff --git a/src/freedreno/vulkan/tu_device.c b/src/freedreno/vulkan/tu_device.c
index 9c09bbd647d..45688837f66 100644
--- a/src/freedreno/vulkan/tu_device.c
+++ b/src/freedreno/vulkan/tu_device.c
@@ -1868,6 +1868,7 @@ tu_CreateDevice(VkPhysicalDevice physicalDevice,
    struct tu6_global *global = device->global_bo->map;
    tu_init_clear_blit_shaders(device);
    global->predicate = 0;
+   global->vtx_stats_query_not_running = 1;
    global->dbg_one = (uint32_t)-1;
    global->dbg_gmem_total_loads = 0;
    global->dbg_gmem_taken_loads = 0;
diff --git a/src/freedreno/vulkan/tu_private.h b/src/freedreno/vulkan/tu_private.h
index 38735010d83..c3dbd7d795b 100644
--- a/src/freedreno/vulkan/tu_private.h
+++ b/src/freedreno/vulkan/tu_private.h
@@ -484,6 +484,8 @@ struct tu6_global
 
    ALIGN16 uint32_t cs_indirect_xyz[3];
 
+   volatile uint32_t vtx_stats_query_not_running;
+
    /* To know when renderpass stats for autotune are valid */
    volatile uint32_t autotune_fence;
 
@@ -1258,6 +1260,12 @@ struct tu_cmd_state
     */
    uint32_t drawcall_bandwidth_per_sample_sum;
 
+   /* VK_QUERY_PIPELINE_STATISTIC_CLIPPING_INVOCATIONS_BIT and
+    * VK_QUERY_TYPE_PRIMITIVES_GENERATED_EXT are allowed to run simultaniously,
+    * but they use the same {START,STOP}_PRIMITIVE_CTRS control.
+    */
+   uint32_t prim_counters_running;
+
    bool prim_generated_query_running_before_rp;
    bool has_prim_generated_query_in_rp;
 
@@ -1304,6 +1312,8 @@ struct tu_cmd_buffer
    VkCommandBufferUsageFlags usage_flags;
    enum tu_cmd_buffer_status status;
 
+   VkQueryPipelineStatisticFlags inherited_pipeline_statistics;
+
    struct tu_cmd_state state;
    uint32_t queue_family_index;
 
diff --git a/src/freedreno/vulkan/tu_query.c b/src/freedreno/vulkan/tu_query.c
index 20d5ee40294..ab003a276e3 100644
--- a/src/freedreno/vulkan/tu_query.c
+++ b/src/freedreno/vulkan/tu_query.c
@@ -426,9 +426,9 @@ statistics_index(uint32_t *statistics)
 }
 
 static bool
-is_pipeline_query_with_vertex_stage(struct tu_query_pool *pool)
+is_pipeline_query_with_vertex_stage(uint32_t pipeline_statistics)
 {
-   return pool->pipeline_statistics &
+   return pipeline_statistics &
           (VK_QUERY_PIPELINE_STATISTIC_INPUT_ASSEMBLY_VERTICES_BIT |
            VK_QUERY_PIPELINE_STATISTIC_INPUT_ASSEMBLY_PRIMITIVES_BIT |
            VK_QUERY_PIPELINE_STATISTIC_VERTEX_SHADER_INVOCATIONS_BIT |
@@ -441,16 +441,16 @@ is_pipeline_query_with_vertex_stage(struct tu_query_pool *pool)
 }
 
 static bool
-is_pipeline_query_with_fragment_stage(struct tu_query_pool *pool)
+is_pipeline_query_with_fragment_stage(uint32_t pipeline_statistics)
 {
-   return pool->pipeline_statistics &
+   return pipeline_statistics &
           VK_QUERY_PIPELINE_STATISTIC_FRAGMENT_SHADER_INVOCATIONS_BIT;
 }
 
 static bool
-is_pipeline_query_with_compute_stage(struct tu_query_pool *pool)
+is_pipeline_query_with_compute_stage(uint32_t pipeline_statistics)
 {
-   return pool->pipeline_statistics &
+   return pipeline_statistics &
           VK_QUERY_PIPELINE_STATISTIC_COMPUTE_SHADER_INVOCATIONS_BIT;
 }
 
@@ -871,15 +871,35 @@ emit_begin_stat_query(struct tu_cmd_buffer *cmdbuf,
    struct tu_cs *cs = cmdbuf->state.pass ? &cmdbuf->draw_cs : &cmdbuf->cs;
    uint64_t begin_iova = pipeline_stat_query_iova(pool, query, begin);
 
-   if (is_pipeline_query_with_vertex_stage(pool)) {
+   if (is_pipeline_query_with_vertex_stage(pool->pipeline_statistics)) {
+      bool need_cond_exec = cmdbuf->state.pass && cmdbuf->state.prim_counters_running;
+      cmdbuf->state.prim_counters_running++;
+
+      /* Prevent starting primitive counters when it is supposed to be stopped
+       * for outer VK_QUERY_TYPE_PRIMITIVES_GENERATED_EXT query.
+       */
+      if (need_cond_exec) {
+         tu_cond_exec_start(cs, CP_COND_REG_EXEC_0_MODE(RENDER_MODE) |
+                        CP_COND_REG_EXEC_0_SYSMEM |
+                        CP_COND_REG_EXEC_0_BINNING);
+      }
+
       tu6_emit_event_write(cmdbuf, cs, START_PRIMITIVE_CTRS);
+
+      tu_cs_emit_pkt7(cs, CP_MEM_WRITE, 3);
+      tu_cs_emit_qw(cs, global_iova(cmdbuf, vtx_stats_query_not_running));
+      tu_cs_emit(cs, 0);
+
+      if (need_cond_exec) {
+         tu_cond_exec_end(cs);
+      }
    }
 
-   if (is_pipeline_query_with_fragment_stage(pool)) {
+   if (is_pipeline_query_with_fragment_stage(pool->pipeline_statistics)) {
       tu6_emit_event_write(cmdbuf, cs, START_FRAGMENT_CTRS);
    }
 
-   if (is_pipeline_query_with_compute_stage(pool)) {
+   if (is_pipeline_query_with_compute_stage(pool->pipeline_statistics)) {
       tu6_emit_event_write(cmdbuf, cs, START_COMPUTE_CTRS);
    }
 
@@ -1008,6 +1028,17 @@ emit_begin_prim_generated_query(struct tu_cmd_buffer *cmdbuf,
       cmdbuf->state.prim_generated_query_running_before_rp = true;
    }
 
+   cmdbuf->state.prim_counters_running++;
+
+   if (cmdbuf->state.pass) {
+      /* Primitives that passed all tests are still counted in in each
+       * tile even with HW binning beforehand. Do not permit it.
+       */
+      tu_cond_exec_start(cs, CP_COND_REG_EXEC_0_MODE(RENDER_MODE) |
+                           CP_COND_REG_EXEC_0_SYSMEM |
+                           CP_COND_REG_EXEC_0_BINNING);
+   }
+
    tu6_emit_event_write(cmdbuf, cs, START_PRIMITIVE_CTRS);
 
    tu_cs_emit_wfi(cs);
@@ -1017,6 +1048,10 @@ emit_begin_prim_generated_query(struct tu_cmd_buffer *cmdbuf,
                   CP_REG_TO_MEM_0_CNT(2) |
                   CP_REG_TO_MEM_0_64B);
    tu_cs_emit_qw(cs, begin_iova);
+
+   if (cmdbuf->state.pass) {
+      tu_cond_exec_end(cs);
+   }
 }
 
 VKAPI_ATTR void VKAPI_CALL
@@ -1152,6 +1187,53 @@ emit_end_occlusion_query(struct tu_cmd_buffer *cmdbuf,
    tu_cs_emit_qw(cs, 0x1);
 }
 
+/* PRIMITIVE_CTRS is used for two distinct queries:
+ * - VK_QUERY_TYPE_PRIMITIVES_GENERATED_EXT
+ * - VK_QUERY_TYPE_PIPELINE_STATISTICS
+ * If one is nested inside other - STOP_PRIMITIVE_CTRS should be emitted
+ * only for outer query.
+ *
+ * Also, pipeline stat query could run outside of renderpass and prim gen
+ * query inside of secondary cmd buffer - for such case we ought to track
+ * the status of pipeline stats query.
+ */
+static void
+emit_stop_primitive_ctrs(struct tu_cmd_buffer *cmdbuf,
+                         struct tu_cs *cs,
+                         enum VkQueryType query_type)
+{
+   bool is_secondary = cmdbuf->vk.level == VK_COMMAND_BUFFER_LEVEL_SECONDARY;
+   cmdbuf->state.prim_counters_running--;
+   if (cmdbuf->state.prim_counters_running == 0) {
+      bool need_cond_exec =
+         is_secondary &&
+         query_type == VK_QUERY_TYPE_PRIMITIVES_GENERATED_EXT &&
+         is_pipeline_query_with_vertex_stage(cmdbuf->inherited_pipeline_statistics);
+
+      if (!need_cond_exec) {
+         tu6_emit_event_write(cmdbuf, cs, STOP_PRIMITIVE_CTRS);
+      } else {
+         tu_cs_reserve(cs, 7 + 2);
+         /* Check that pipeline stats query is not running, only then
+          * we count stop the counter.
+          */
+         tu_cs_emit_pkt7(cs, CP_COND_EXEC, 6);
+         tu_cs_emit_qw(cs, global_iova(cmdbuf, vtx_stats_query_not_running));
+         tu_cs_emit_qw(cs, global_iova(cmdbuf, vtx_stats_query_not_running));
+         tu_cs_emit(cs, CP_COND_EXEC_4_REF(0x2));
+         tu_cs_emit(cs, 2); /* Cond execute the next 2 DWORDS */
+
+         tu6_emit_event_write(cmdbuf, cs, STOP_PRIMITIVE_CTRS);
+      }
+   }
+
+   if (query_type == VK_QUERY_TYPE_PIPELINE_STATISTICS) {
+      tu_cs_emit_pkt7(cs, CP_MEM_WRITE, 3);
+      tu_cs_emit_qw(cs, global_iova(cmdbuf, vtx_stats_query_not_running));
+      tu_cs_emit(cs, 1);
+   }
+}
+
 static void
 emit_end_stat_query(struct tu_cmd_buffer *cmdbuf,
                     struct tu_query_pool *pool,
@@ -1164,15 +1246,19 @@ emit_end_stat_query(struct tu_cmd_buffer *cmdbuf,
    uint64_t stat_start_iova;
    uint64_t stat_stop_iova;
 
-   if (is_pipeline_query_with_vertex_stage(pool)) {
-      tu6_emit_event_write(cmdbuf, cs, STOP_PRIMITIVE_CTRS);
+   if (is_pipeline_query_with_vertex_stage(pool->pipeline_statistics)) {
+      /* No need to conditionally execute STOP_PRIMITIVE_CTRS when
+       * we are inside VK_QUERY_TYPE_PRIMITIVES_GENERATED_EXT inside of a
+       * renderpass, because it is already stopped.
+       */
+      emit_stop_primitive_ctrs(cmdbuf, cs, VK_QUERY_TYPE_PIPELINE_STATISTICS);
    }
 
-   if (is_pipeline_query_with_fragment_stage(pool)) {
+   if (is_pipeline_query_with_fragment_stage(pool->pipeline_statistics)) {
       tu6_emit_event_write(cmdbuf, cs, STOP_FRAGMENT_CTRS);
    }
 
-   if (is_pipeline_query_with_compute_stage(pool)) {
+   if (is_pipeline_query_with_compute_stage(pool->pipeline_statistics)) {
       tu6_emit_event_write(cmdbuf, cs, STOP_COMPUTE_CTRS);
    }
 
@@ -1355,7 +1441,11 @@ emit_end_prim_generated_query(struct tu_cmd_buffer *cmdbuf,
    uint64_t result_iova = primitives_generated_query_iova(pool, query, result);
    uint64_t available_iova = query_available_iova(pool, query);
 
-   tu6_emit_event_write(cmdbuf, cs, STOP_PRIMITIVE_CTRS);
+   if (cmdbuf->state.pass) {
+      tu_cond_exec_start(cs, CP_COND_REG_EXEC_0_MODE(RENDER_MODE) |
+                             CP_COND_REG_EXEC_0_SYSMEM |
+                             CP_COND_REG_EXEC_0_BINNING);
+   }
 
    tu_cs_emit_wfi(cs);
 
@@ -1375,6 +1465,15 @@ emit_end_prim_generated_query(struct tu_cmd_buffer *cmdbuf,
 
    tu_cs_emit_pkt7(cs, CP_WAIT_MEM_WRITES, 0);
 
+   /* Should be after waiting for mem writes to have up to date info
+    * about which query is running.
+    */
+   emit_stop_primitive_ctrs(cmdbuf, cs, VK_QUERY_TYPE_PRIMITIVES_GENERATED_EXT);
+
+   if (cmdbuf->state.pass) {
+      tu_cond_exec_end(cs);
+   }
+
    if (cmdbuf->state.pass)
       cs = &cmdbuf->draw_epilogue_cs;
 
diff --git a/src/gallium/drivers/zink/ci/zink-tu-a630-flakes.txt b/src/gallium/drivers/zink/ci/zink-tu-a630-flakes.txt
index 8d342317bd0..268c4c5dc19 100644
--- a/src/gallium/drivers/zink/ci/zink-tu-a630-flakes.txt
+++ b/src/gallium/drivers/zink/ci/zink-tu-a630-flakes.txt
@@ -1,6 +1,3 @@
-# #6603
-GTF-GL46.gtf40.GL3Tests.transform_feedback2.transform_feedback2_states
-
 GTF-GL46.gtf32.GL3Tests.packed_pixels.packed_pixels_pixelstore
 KHR-Single-GL46.arrays_of_arrays_gl.ConstructorsAndUnsizedDeclConstructorSizing1
 dEQP-GLES2.functional.shaders.indexing.matrix_subscript.mat4_dynamic_write_dynamic_read_vertex