BUG: Add fillna at the beginning of _where not to fill NA. #60729

doc/source/whatsnew/v3.0.0.rst

@@ -697,6 +697,7 @@ Indexing
 - Bug in :meth:`DataFrame.from_records` throwing a ``ValueError`` when passed an empty list in ``index`` (:issue:`58594`)
 - Bug in :meth:`DataFrame.loc` with inconsistent behavior of loc-set with 2 given indexes to Series (:issue:`59933`)
 - Bug in :meth:`MultiIndex.insert` when a new value inserted to a datetime-like level gets cast to ``NaT`` and fails indexing (:issue:`60388`)
+- Bug in :meth:`Series.mask` unexpectedly filling ``pd.NA`` (:issue:`60729`)
 - Bug in printing :attr:`Index.names` and :attr:`MultiIndex.levels` would not escape single quotes (:issue:`60190`)
 
 Missing

pandas/core/generic.py

@@ -9701,6 +9701,7 @@ def _where(
         # align the cond to same shape as myself
         cond = common.apply_if_callable(cond, self)
         if isinstance(cond, NDFrame):
+            cond = cond.fillna(True)
             # CoW: Make sure reference is not kept alive
             if cond.ndim == 1 and self.ndim == 2:
                 cond = cond._constructor_expanddim(
@@ -9712,6 +9713,9 @@ def _where(
         else:
             if not hasattr(cond, "shape"):
                 cond = np.asanyarray(cond)
+            else:
+                cond = np.array(cond)
+            cond[isna(cond)] = True
             if cond.shape != self.shape:
                 raise ValueError("Array conditional must be same shape as self")
             cond = self._constructor(cond, **self._construct_axes_dict(), copy=False)

pandas/tests/series/indexing/test_mask.py

@@ -1,6 +1,8 @@
 import numpy as np
 import pytest
 
+import pandas.util._test_decorators as td
+
 from pandas import Series
 import pandas._testing as tm
 
@@ -67,3 +69,19 @@ def test_mask_inplace():
     rs = s.copy()
     rs.mask(cond, -s, inplace=True)
     tm.assert_series_equal(rs, s.mask(cond, -s))
+
+
+@pytest.mark.parametrize(
+    "dtype",
+    [
+        "Int64",
+        pytest.param("int64[pyarrow]", marks=td.skip_if_no("pyarrow")),
+    ],
+)
+def test_mask_na(dtype):
+    # We should not be filling pd.NA. See GH#60729
+    series = Series([None, 1, 2, None, 3, 4, None], dtype=dtype)
+    result = series.mask(series <= 2, -99)
+    expected = Series([None, -99, -99, None, 3, 4, None], dtype=dtype)
+
+    tm.assert_series_equal(result, expected)