diff --git a/tests/pytorch/test_fused_router.py b/tests/pytorch/test_fused_router.py
index 274a35b81d..f54d16abe2 100644
--- a/tests/pytorch/test_fused_router.py
+++ b/tests/pytorch/test_fused_router.py
@@ -414,17 +414,20 @@ def test_fused_scores_for_aux_loss(dtype, num_tokens, num_experts, topk, score_f
 @pytest.mark.parametrize("num_tokens", [2048, 7168, 14234])
 @pytest.mark.parametrize("num_experts", [1024, 256, 128, 32])
 @pytest.mark.parametrize("topk", [4, 32])
-def test_fused_moe_aux_loss(dtype, num_tokens, num_experts, topk):
+@pytest.mark.parametrize("expert_multiplier", [1, 2])
+def test_fused_moe_aux_loss(dtype, num_tokens, num_experts, topk, expert_multiplier):
     if topk >= num_experts:
         pytest.skip(f"topk ({topk}) >= num_experts ({num_experts})")
+    # Sequence aux loss batches independent sequences along the expert dimension.
+    num_cols = num_experts * expert_multiplier
     # Construct the special probs to avoid inf in the sigmoid function
     offset = torch.arange(-num_tokens // 2, num_tokens // 2, dtype=dtype, device="cuda") * 1e-4
-    probs = torch.arange(-num_experts // 2, num_experts // 2, device="cuda", dtype=dtype) * 1e-2
+    probs = torch.arange(-num_cols // 2, num_cols // 2, device="cuda", dtype=dtype) * 1e-2
     probs = probs.unsqueeze(0).repeat(num_tokens, 1) + offset.unsqueeze(1)
-    probs = probs.view(num_tokens, num_experts)
+    probs = probs.view(num_tokens, num_cols)
     probs.requires_grad = True
 
-    tokens_per_expert = torch.randint(1, 1000, (num_experts,), device="cuda", dtype=torch.int32)
+    tokens_per_expert = torch.randint(1, 1000, (num_cols,), device="cuda", dtype=torch.int32)
     coeff = 0.01
 
     probs_clone = deepcopy(probs)
@@ -448,7 +451,7 @@ def test_fused_moe_aux_loss(dtype, num_tokens, num_experts, topk):
         coeff=coeff,
     )
 
-    atol, rtol = _get_tolerances(dtype, num_experts)
+    atol, rtol = _get_tolerances(dtype, num_cols)
     torch.testing.assert_close(aux_loss, aux_loss_fused, atol=atol, rtol=rtol)
 
     # Backward
diff --git a/transformer_engine/common/fused_router/fused_moe_aux_loss.cu b/transformer_engine/common/fused_router/fused_moe_aux_loss.cu
index 7e516af97b..cc5e5e3bcc 100644
--- a/transformer_engine/common/fused_router/fused_moe_aux_loss.cu
+++ b/transformer_engine/common/fused_router/fused_moe_aux_loss.cu
@@ -87,8 +87,11 @@ void fused_moe_aux_loss_forward_kernel_launcher(const DataType* probs,
                                                 int num_cols, int topk, float coeff,
                                                 DataType* aux_loss, float* Coeff_buf,
                                                 cudaStream_t stream) {
-  NVTE_CHECK(num_experts == num_cols, "Number of experts (", num_experts,
-             ") must be equal to number of input columns (", num_cols, ").");
+  NVTE_CHECK(num_cols > 0, "num_cols must be positive, got ", num_cols);
+  NVTE_CHECK(num_experts > 0, "num_experts must be positive, got ", num_experts);
+  // Sequence aux loss batches independent sequences along the expert dimension.
+  NVTE_CHECK(num_cols % num_experts == 0, "Number of input columns (", num_cols,
+             ") must be a multiple of number of experts (", num_experts, ").");
 
   // Round up to a multiple of warp size for correct warp shuffles.
   const int block_size = ((std::min(1024, num_cols) + static_cast<int>(kThreadsPerWarp) - 1) /
@@ -98,7 +101,7 @@ void fused_moe_aux_loss_forward_kernel_launcher(const DataType* probs,
 
   // One CompType per thread in shared memory.
   const size_t smem_size = block_size * sizeof(CompType);
-  check_shared_memory_capacity_num_experts(smem_size, num_experts);
+  check_shared_memory_capacity_num_experts(smem_size, num_cols);
 
   // Compute final coefficient and zero the float accumulator (Coeff_buf[1]) before launch.
   const float C_coeff = (num_experts * coeff) / topk / total_num_tokens / total_num_tokens;