diff --git a/src/plugins/intel_cpu/src/emitters/snippets/x64/kernel_executors/brgemm.cpp b/src/plugins/intel_cpu/src/emitters/snippets/x64/kernel_executors/brgemm.cpp
index aa917c89dcb016..e46de866990005 100644
--- a/src/plugins/intel_cpu/src/emitters/snippets/x64/kernel_executors/brgemm.cpp
+++ b/src/plugins/intel_cpu/src/emitters/snippets/x64/kernel_executors/brgemm.cpp
@@ -224,9 +224,12 @@ void BrgemmKernelExecutor::update_config(const ov::snippets::lowered::Expression
         // Quick validation check: Should we check that port is really Brgemm port?
         // If BrgemmCopyB in the Loop by M -> first input port will be BrgemmCopyB with `incremented=false`
         // to avoid extra checks, we validate only first input port
-        OPENVINO_ASSERT(in_ports.size() > 1 && in_ports.front().is_incremented && in_ports.front().dim_idx == 1 &&
-                        out_ports.size() == 1 && out_ports.front().is_incremented && out_ports.front().dim_idx == 1,
-                        "Incorrect Loop by Brgemm dimension N");
+        // Note: We check `is_incremented` attribute only for not incremented ports because
+        //       this `is_incremented = true` can be changed by `CleanRepeatedDataPointerShifts` optimization
+        auto check_port = [&](const ov::snippets::lowered::LoopPort& p) { return p.dim_idx == 1; };
+        OPENVINO_ASSERT(in_ports.size() > 1 && std::all_of(in_ports.cbegin(), in_ports.cend(), check_port) &&
+                        out_ports.size() == 1 && check_port(out_ports.back()),
+                        "Incorrect Loop by Brgemm dimension M");
         M = current_expanded_loop_info->get_increment();
         input_pds[0]->set_subtensor_dim(1, M);
         output_pds[0]->set_subtensor_dim(1, M);
@@ -240,8 +243,11 @@ void BrgemmKernelExecutor::update_config(const ov::snippets::lowered::Expression
         const auto& in_ports = current_expanded_loop_info->get_input_ports();
         const auto& out_ports = current_expanded_loop_info->get_output_ports();
         // Quick validation check: Should we check that port is really Brgemm port?
-        OPENVINO_ASSERT(in_ports.size() == 2 && !in_ports.front().is_incremented && in_ports.back().is_incremented && in_ports.back().dim_idx == 0 &&
-                        out_ports.size() == 1 && out_ports.front().is_incremented && out_ports.front().dim_idx == 0,
+        // Note: We check `is_incremented` attribute only for not incremented ports because
+        //       this `is_incremented = true` can be changed by `CleanRepeatedDataPointerShifts` optimization
+        auto check_port = [&](const ov::snippets::lowered::LoopPort& p) { return p.dim_idx == 0; };
+        OPENVINO_ASSERT(in_ports.size() == 2 && !in_ports.front().is_incremented && std::all_of(in_ports.cbegin(), in_ports.cend(), check_port) &&
+                        out_ports.size() == 1 && check_port(out_ports.back()),
                         "Incorrect Loop by Brgemm dimension N");
         N = current_expanded_loop_info->get_increment();
         input_pds[1]->set_subtensor_dim(0, N);
@@ -261,8 +267,9 @@ void BrgemmKernelExecutor::update_config(const ov::snippets::lowered::Expression
         const auto& in_ports = current_expanded_loop_info->get_input_ports();
         const auto& out_ports = current_expanded_loop_info->get_output_ports();
         // Quick validation check: Should we check that port is really Brgemm port?
-        OPENVINO_ASSERT(in_ports.size() == 2 && in_ports.front().is_incremented && in_ports.front().dim_idx == 0 &&
-                                                in_ports.back().is_incremented && in_ports.back().dim_idx == 1 &&
+        // Note: We check `is_incremented` attribute only for not incremented ports because
+        //       this `is_incremented = true` can be changed by `CleanRepeatedDataPointerShifts` optimization
+        OPENVINO_ASSERT(in_ports.size() == 2 && in_ports.front().dim_idx == 0 && in_ports.back().dim_idx == 1 &&
                         out_ports.size() == 1 && !out_ports.front().is_incremented,
                         "Incorrect Loop by Brgemm dimension K");
         K = current_expanded_loop_info->get_increment();
diff --git a/src/plugins/intel_cpu/tests/functional/shared_tests_instances/snippets/mha.cpp b/src/plugins/intel_cpu/tests/functional/shared_tests_instances/snippets/mha.cpp
index c5ee28757b0e04..380967a44f5fa6 100644
--- a/src/plugins/intel_cpu/tests/functional/shared_tests_instances/snippets/mha.cpp
+++ b/src/plugins/intel_cpu/tests/functional/shared_tests_instances/snippets/mha.cpp
@@ -25,7 +25,8 @@ const auto& inputShapes_4D = STATIC_SHAPES(
 
 const auto& inputShapes_3D = STATIC_SHAPES(
     {{128, 12, 64}, {128, 12, 64}, {12, 128, 128}, {128, 12, 64}},
-    {{68, 6, 92}, {68, 6, 92}, {1, 68, 68}, {68, 6, 92}});
+    {{68, 6, 92}, {68, 6, 92}, {1, 68, 68}, {68, 6, 92}},
+    {{16, 2, 92}, {68, 2, 92}, {1, 16, 68}, {68, 2, 92}});
 
 static inline bool is_bf16_supported() {
     return ov::with_cpu_x86_bfloat16() || ov::with_cpu_x86_avx512_core_amx_bf16();