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

doc/source/whatsnew/v3.0.0.rst

@@ -676,6 +676,7 @@ Interval
 
 Indexing
 ^^^^^^^^
+- Bug in :func:`Series.mask` unexpectedly filling pd.NA (:issue:`60729`)
 - Bug in :meth:`DataFrame.__getitem__` returning modified columns when called with ``slice`` in Python 3.12 (:issue:`57500`)
 - Bug in :meth:`DataFrame.from_records` throwing a ``ValueError`` when passed an empty list in ``index`` (:issue:`58594`)
 - Bug in :meth:`MultiIndex.insert` when a new value inserted to a datetime-like level gets cast to ``NaT`` and fails indexing (:issue:`60388`)

pandas/core/generic.py

@@ -9674,6 +9674,13 @@ def _where(
         if axis is not None:
             axis = self._get_axis_number(axis)
 
+        # We should not be filling NA. See GH#60729
+        if isinstance(cond, np.ndarray):
+            cond = np.array(cond)
+            cond[np.isnan(cond)] = True
+        elif isinstance(cond, NDFrame):
+            cond = cond.fillna(True)
+
         # align the cond to same shape as myself
         cond = common.apply_if_callable(cond, self)
         if isinstance(cond, NDFrame):

pandas/tests/series/indexing/test_mask.py

@@ -1,7 +1,10 @@
 import numpy as np
 import pytest
 
-from pandas import Series
+from pandas import (
+    Int64Dtype,
+    Series,
+)
 import pandas._testing as tm
 
 
@@ -67,3 +70,12 @@ def test_mask_inplace():
     rs = s.copy()
     rs.mask(cond, -s, inplace=True)
     tm.assert_series_equal(rs, s.mask(cond, -s))
+
+
+def test_mask_na():
+    # We should not be filling pd.NA. See GH#60729
+    series = Series([None, 1, 2, None, 3, 4, None], dtype=Int64Dtype())
+    result = series.mask(series <= 2, -99)
+    expected = Series([None, -99, -99, None, 3, 4, None], dtype=Int64Dtype())
+
+    tm.assert_series_equal(result, expected)