diff --git a/transformer_engine/common/triton/permutation.py b/transformer_engine/common/triton/permutation.py
index 4602f41cfd..147742bb05 100644
--- a/transformer_engine/common/triton/permutation.py
+++ b/transformer_engine/common/triton/permutation.py
@@ -563,6 +563,13 @@ def _make_chunk_sort_map_kernel(
         split_sizes_ptr + load_split_offset, mask=load_split_offset < num_splits, other=0
     ).to(tl.int32)
     input_split_sizes_cumsum = tl.cumsum(input_split_sizes)
+
+    # Compute total valid tokens and skip phantom/padding tokens.
+    # When the input buffer is larger than sum(split_sizes), tokens beyond
+    # the valid range should map to themselves (identity mapping) to avoid
+    # corrupting valid output positions.
+    total_valid_tokens = tl.sum(input_split_sizes)
+
     input_split_sizes_mask = tl.where(input_split_sizes_cumsum <= pid, 1, 0)
     input_chunk_idx = tl.sum(input_split_sizes_mask)
     input_split_sizes_presum = tl.sum(input_split_sizes * input_split_sizes_mask)
@@ -578,6 +585,11 @@ def _make_chunk_sort_map_kernel(
     ).to(tl.int32)
     output_pre_split_sizes = tl.where(load_split_offset < output_chunk_idx, output_split_sizes, 0)
     dst_row = tl.sum(output_pre_split_sizes) + in_chunk_offset
+
+    # For tokens beyond the valid range (pid >= total_valid_tokens),
+    # use identity mapping to avoid corrupting valid data
+    dst_row = tl.where(pid < total_valid_tokens, dst_row, pid)
+
     tl.store(dst_rows_ptr + pid, dst_row)
 
 
diff --git a/transformer_engine/jax/permutation.py b/transformer_engine/jax/permutation.py
index 438511fa55..6a0a3229d9 100644
--- a/transformer_engine/jax/permutation.py
+++ b/transformer_engine/jax/permutation.py
@@ -581,7 +581,7 @@ def sort_chunks_by_index(
     return _sort_chunks_by_index(inp, split_sizes, sorted_indices)
 
 
-@partial(jax.custom_vjp, nondiff_argnums=(1, 2))
+@jax.custom_vjp
 def _sort_chunks_by_index(
     inp: jnp.ndarray,
     split_sizes: jnp.ndarray,
@@ -596,7 +596,7 @@ def _sort_chunks_by_index_fwd_rule(
     inp: jnp.ndarray,
     split_sizes: jnp.ndarray,
     sorted_indices: jnp.ndarray,
-) -> Tuple[Tuple[jnp.ndarray, jnp.ndarray], Tuple[jnp.ndarray, int, int]]:
+) -> Tuple[Tuple[jnp.ndarray, jnp.ndarray], Tuple[jnp.ndarray, jnp.ndarray, jnp.ndarray, int, int]]:
     """Forward pass rule for sort_chunks_by_index."""
     # Validate input dimensions
     assert inp.ndim in [2, 3], f"inp must be 2D or 3D, got {inp.ndim}D"
@@ -618,18 +618,17 @@ def _sort_chunks_by_index_fwd_rule(
     )
 
     # Return (primals, residuals)
-    residuals = (row_id_map, num_tokens, hidden_size)
+    # Include split_sizes and sorted_indices in residuals since we removed nondiff_argnums
+    residuals = (row_id_map, split_sizes, sorted_indices, num_tokens, hidden_size)
     return (output, row_id_map), residuals
 
 
 def _sort_chunks_by_index_bwd_rule(
-    _split_sizes: jnp.ndarray,
-    _sorted_indices: jnp.ndarray,
-    residuals: Tuple[jnp.ndarray, int, int],
+    residuals: Tuple[jnp.ndarray, jnp.ndarray, jnp.ndarray, int, int],
     g: Tuple[jnp.ndarray, jnp.ndarray],
-) -> Tuple[jnp.ndarray]:
+) -> Tuple[jnp.ndarray, jnp.ndarray, jnp.ndarray]:
     """Backward pass rule for sort_chunks_by_index."""
-    row_id_map, num_tokens, hidden_size = residuals
+    row_id_map, split_sizes, sorted_indices, num_tokens, hidden_size = residuals
     output_grad, _ = g
 
     # Backward: reverse the sort
@@ -642,7 +641,12 @@ def _sort_chunks_by_index_bwd_rule(
         is_forward=False,
     )
 
-    return (inp_grad,)
+    # Return gradients for all inputs: (inp, split_sizes, sorted_indices)
+    # split_sizes and sorted_indices are integer arrays, so their gradients are zeros
+    split_sizes_grad = jnp.zeros_like(split_sizes, dtype=split_sizes.dtype)
+    sorted_indices_grad = jnp.zeros_like(sorted_indices, dtype=sorted_indices.dtype)
+
+    return (inp_grad, split_sizes_grad, sorted_indices_grad)
 
 
 _sort_chunks_by_index.defvjp(_sort_chunks_by_index_fwd_rule, _sort_chunks_by_index_bwd_rule)