diff --git a/src/zarr/core/buffer/core.py b/src/zarr/core/buffer/core.py
index 0c6d966db9..ba629befa1 100644
--- a/src/zarr/core/buffer/core.py
+++ b/src/zarr/core/buffer/core.py
@@ -462,8 +462,12 @@ def __len__(self) -> int:
     def __repr__(self) -> str:
         return f"<NDBuffer shape={self.shape} dtype={self.dtype} {self._data!r}>"
 
-    def all_equal(self, other: Any) -> bool:
-        return bool((self._data == other).all())
+    def all_equal(self, other: Any, equal_nan: bool = True) -> bool:
+        """Compare to `other` using np.array_equal."""
+        # use array_equal to obtain equal_nan=True functionality
+        data, other = np.broadcast_arrays(self._data, other)
+        result = np.array_equal(self._data, other, equal_nan=equal_nan)
+        return result
 
     def fill(self, value: Any) -> None:
         self._data.fill(value)
diff --git a/tests/v3/test_array.py b/tests/v3/test_array.py
index 11be51682c..b7beb63b1c 100644
--- a/tests/v3/test_array.py
+++ b/tests/v3/test_array.py
@@ -138,6 +138,25 @@ def test_array_v3_fill_value(store: MemoryStore, fill_value: int, dtype_str: str
     assert arr.fill_value.dtype == arr.dtype
 
 
+@pytest.mark.parametrize("store", ["memory"], indirect=True)
+async def test_array_v3_nan_fill_value(store: MemoryStore) -> None:
+    shape = (10,)
+    arr = Array.create(
+        store=store,
+        shape=shape,
+        dtype=np.float64,
+        zarr_format=3,
+        chunk_shape=shape,
+        fill_value=np.nan,
+    )
+    arr[:] = np.nan
+
+    assert np.isnan(arr.fill_value)
+    assert arr.fill_value.dtype == arr.dtype
+    # all fill value chunk is an empty chunk, and should not be written
+    assert len([a async for a in store.list_prefix("/")]) == 0
+
+
 @pytest.mark.parametrize("store", ("local",), indirect=["store"])
 @pytest.mark.parametrize("zarr_format", (2, 3))
 async def test_serializable_async_array(
diff --git a/tests/v3/test_properties.py b/tests/v3/test_properties.py
index 7a085c03b7..a78e9207bd 100644
--- a/tests/v3/test_properties.py
+++ b/tests/v3/test_properties.py
@@ -18,11 +18,6 @@ def test_roundtrip(data: st.DataObject) -> None:
 
 
 @given(data=st.data())
-# The filter warning here is to silence an occasional warning in NDBuffer.all_equal
-# See https://github.com/zarr-developers/zarr-python/pull/2118#issuecomment-2310280899
-# Uncomment the next line to reproduce the original failure.
-# @reproduce_failure('6.111.2', b'AXicY2FgZGRAB/8/ndR2z7nkDZEDADWpBL4=')
-@pytest.mark.filterwarnings("ignore::RuntimeWarning")
 def test_basic_indexing(data: st.DataObject) -> None:
     zarray = data.draw(arrays())
     nparray = zarray[:]
@@ -37,11 +32,6 @@ def test_basic_indexing(data: st.DataObject) -> None:
 
 
 @given(data=st.data())
-# The filter warning here is to silence an occasional warning in NDBuffer.all_equal
-# See https://github.com/zarr-developers/zarr-python/pull/2118#issuecomment-2310280899
-# Uncomment the next line to reproduce the original failure.
-# @reproduce_failure('6.111.2', b'AXicY2FgZGRAB/8/eLmF7qr/C5EDADZUBRM=')
-@pytest.mark.filterwarnings("ignore::RuntimeWarning")
 def test_vindex(data: st.DataObject) -> None:
     zarray = data.draw(arrays())
     nparray = zarray[:]