diff --git a/test/test_pallas.py b/test/test_pallas.py
index 8c96bae0301..4c291de3acc 100644
--- a/test/test_pallas.py
+++ b/test/test_pallas.py
@@ -242,6 +242,21 @@ def test_flash_attention_wrapper(self):
     expected_o = self._attention(q, k, v)
     self.assertTrue(torch.allclose(o.cpu(), expected_o.cpu(), atol=1e-05))
 
+  @unittest.skipIf(xr.device_type() != 'TPU' or tpu.version() < 3,
+                   "This test only works on TPUv3+.")
+  @with_jax_high_precision
+  def test_flash_attention_wrapper_kv_and_ab_padding(self):
+    from torch_xla.experimental.custom_kernel import flash_attention
+
+    q = torch.randn(1, 2, 513, 4).to("xla")
+    k = torch.randn(1, 2, 513, 4).to("xla")
+    v = torch.randn(1, 2, 513, 4).to("xla")
+    ab = torch.randn(1, 2, 513, 513).to("xla")
+
+    o = flash_attention(q, k, v, ab=ab)
+    expected_o = self._attention(q, k, v, ab=ab)
+    self.assertTrue(torch.allclose(o.cpu(), expected_o.cpu(), atol=1e-05))
+
   @unittest.skipIf(xr.device_type() != 'TPU' or tpu.version() < 3,
                    "This test only works on TPUv3+.")
   @with_jax_high_precision
diff --git a/test/test_pallas_spmd.py b/test/test_pallas_spmd.py
index ba9b819c653..f9a48aab7fb 100644
--- a/test/test_pallas_spmd.py
+++ b/test/test_pallas_spmd.py
@@ -77,6 +77,26 @@ def test_flash_attention_spmd_data_parallel(self):
     expected_o = self._attention(q, k, v)
     self.assertTrue(torch.allclose(o.cpu(), expected_o.cpu(), atol=1e-05))
 
+  @unittest.skipIf(xr.device_type() != 'TPU' or tpu.version() < 3,
+                   "This test only works on TPUv3+.")
+  @with_jax_high_precision
+  def test_flash_attention_spmd_data_parallel_kv_and_ab_padding(self):
+    n_devices = xr.global_runtime_device_count()
+    xs.set_global_mesh(xs.Mesh(range(n_devices), (n_devices, 1, 1, 1)))
+
+    q = torch.randn(4, 2, 513, 4).to("xla")
+    k = torch.randn(4, 2, 513, 4).to("xla")
+    v = torch.randn(4, 2, 513, 4).to("xla")
+    ab = torch.randn(4, 2, 513, 513).to("xla")
+
+    o = flash_attention(q, k, v, ab=ab, partition_spec=range(n_devices))
+    self.assertEqual(
+        torch_xla._XLAC._get_xla_sharding_spec(o),
+        f"{{devices=[{n_devices},1,1,1]0,1,2,3}}")
+
+    expected_o = self._attention(q, k, v, ab=ab)
+    self.assertTrue(torch.allclose(o.cpu(), expected_o.cpu(), atol=1e-05))
+
   @unittest.skipIf(xr.device_type() != 'TPU' or tpu.version() < 3,
                    "This test only works on TPUv3+.")
   @with_jax_high_precision
diff --git a/torch_xla/experimental/custom_kernel.py b/torch_xla/experimental/custom_kernel.py
index 45c7a4a6de0..e5299683951 100644
--- a/torch_xla/experimental/custom_kernel.py
+++ b/torch_xla/experimental/custom_kernel.py
@@ -248,6 +248,18 @@ def fa_custom_forward(
     full_ab = ab.clone()
   else:
     full_ab = None
+
+  block_k_major = min(FlashAttention.DEFAULT_BLOCK_SIZES["block_k_major"],
+                      k.shape[2])
+  block_k = min(FlashAttention.DEFAULT_BLOCK_SIZES["block_k"], k.shape[2])
+  k, k_pad_size = _pad_to_block_size(k, max(block_k_major, block_k), 2)
+  if k_pad_size > 0:
+    v, _ = _pad_to_block_size(v, max(block_k_major, block_k), 2)
+    if ab is None:
+      ab = torch.zeros((q.shape[0], q.shape[1], q.shape[2], q.shape[2]))
+    ab, _ = _pad_to_block_size(
+        ab, max(block_k_major, block_k), 3, padding_minus_inf=True)
+
   if partition_spec is not None:
     q_full_shape = q.shape
     q = xs.enable_manual_sharding(q, partition_spec, mesh=mesh).global_tensor
@@ -295,8 +307,8 @@ def fa_custom_forward(
         sm_scale,
         min(FlashAttention.DEFAULT_BLOCK_SIZES["block_b"], q.shape[0]),
         min(FlashAttention.DEFAULT_BLOCK_SIZES["block_q"], q.shape[2]),
-        min(FlashAttention.DEFAULT_BLOCK_SIZES["block_k_major"], k.shape[2]),
-        min(FlashAttention.DEFAULT_BLOCK_SIZES["block_k"], k.shape[2]),
+        block_k_major,
+        block_k,
         False,
         static_argnums=range(5, 13),
         use_cache=True,
@@ -337,6 +349,27 @@ def fa_custom_forward(
   return tuple(outs)
 
 
+def _pad_to_block_size(
+    tensor: torch.Tensor,
+    block_size: int,
+    dim: int,
+    padding_minus_inf: bool = False) -> Tuple[torch.Tensor, int]:
+  size = tensor.shape[dim]
+  if size % block_size == 0:
+    return tensor, 0
+
+  pad_size = block_size - (size % block_size)
+  pad_shape = list(tensor.shape)
+  pad_shape[dim] = pad_size
+  padding = torch.full(
+      pad_shape,
+      torch.finfo(tensor.dtype).min if padding_minus_inf else 0,
+      dtype=tensor.dtype,
+      device=tensor.device)
+  padded = torch.cat([tensor, padding], dim=dim)
+  return padded, pad_size
+
+
 @custom_op("xla::fa_custom_backward", mutates_args=())
 def fa_custom_backward(
     grad_output: torch.Tensor, q: torch.Tensor, k: torch.Tensor,