diff --git a/doc/source/whatsnew/v3.0.0.rst b/doc/source/whatsnew/v3.0.0.rst
index bebd928924214..3f37610a11064 100644
--- a/doc/source/whatsnew/v3.0.0.rst
+++ b/doc/source/whatsnew/v3.0.0.rst
@@ -1192,6 +1192,7 @@ Indexing
 - Bug in :meth:`Index.get_indexer` and similar methods when ``NaN`` is located at or after position 128 (:issue:`58924`)
 - 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.__setitem__` when assigning boolean series with boolean indexer will raise ``LossySetitemError`` (:issue:`57338`)
+- Bug in :meth:`Series.mask` unexpectedly filling ``pd.NA`` (:issue:`60729`)
 - Bug in indexing ``obj.loc[start:stop]`` with a :class:`DatetimeIndex` and :class:`Timestamp` endpoints with higher resolution than the index (:issue:`63262`)
 - Bug in printing :attr:`Index.names` and :attr:`MultiIndex.levels` would not escape single quotes (:issue:`60190`)
 - Bug in reindexing of :class:`DataFrame` with :class:`PeriodDtype` columns in case of consolidated block (:issue:`60980`, :issue:`60273`)
diff --git a/pandas/core/generic.py b/pandas/core/generic.py
index 79f682988a148..8e0bfe56131c5 100644
--- a/pandas/core/generic.py
+++ b/pandas/core/generic.py
@@ -9631,6 +9631,7 @@ 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(
@@ -9645,6 +9646,7 @@ def _where(
             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)
+            cond = cond.fillna(True)
 
         # make sure we are boolean
         fill_value = bool(inplace)
@@ -9992,6 +9994,18 @@ def mask(
         if not hasattr(cond, "__invert__"):
             cond = np.array(cond)
 
+        # GH 60772
+        na_msg = "Cannot mask with non-boolean array containing NA / NaN values"
+        if isinstance(cond, np.ndarray):
+            if not lib.is_bool_array(cond):
+                raise ValueError(na_msg)
+        elif isinstance(cond, ABCDataFrame):
+            if not all(is_bool_dtype(blk.dtype) for blk in cond._mgr.blocks):
+                raise ValueError(na_msg)
+        elif isinstance(cond, ABCSeries):
+            if not is_bool_dtype(cond):
+                raise ValueError(na_msg)
+
         return self._where(
             ~cond,
             other=other,
diff --git a/pandas/tests/series/indexing/test_mask.py b/pandas/tests/series/indexing/test_mask.py
index 3c21cd0d5ca64..75c44e6d56399 100644
--- a/pandas/tests/series/indexing/test_mask.py
+++ b/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 +69,31 @@ 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")),
+    ],
+)
+@pytest.mark.parametrize("cond_type", [["series", "list", "numpy"]])
+def test_mask_na(dtype, cond_type):
+    # We should not be filling pd.NA. See GH#60729
+    series = Series([None, 1, 2, None, 3, 4, None], dtype=dtype)
+    cond = series <= 2
+
+    if cond_type == "list":
+        cond = cond.to_list()
+    elif cond_type == "numpy":
+        cond = cond.to_numpy()
+
+    if isinstance(cond, Series):
+        result = series.mask(cond, -99)
+        expected = Series([None, -99, -99, None, 3, 4, None], dtype=dtype)
+        tm.assert_series_equal(result, expected)
+    else:
+        msg = "Cannot mask with non-boolean array containing NA / NaN values"
+        with pytest.raises(ValueError, match=msg):
+            series.mask(cond)
diff --git a/pandas/tests/series/indexing/test_where.py b/pandas/tests/series/indexing/test_where.py
index ec8c15714bf82..52bebfe6a2520 100644
--- a/pandas/tests/series/indexing/test_where.py
+++ b/pandas/tests/series/indexing/test_where.py
@@ -1,6 +1,8 @@
 import numpy as np
 import pytest
 
+import pandas.util._test_decorators as td
+
 from pandas.core.dtypes.common import is_integer
 
 import pandas as pd
@@ -445,3 +447,25 @@ def test_where_datetimelike_categorical(tz_naive_fixture):
     res = pd.DataFrame(lvals).where(mask[:, None], pd.DataFrame(rvals))
 
     tm.assert_frame_equal(res, pd.DataFrame(dr))
+
+
+@pytest.mark.parametrize(
+    "dtype",
+    [
+        "Int64",
+        pytest.param("int64[pyarrow]", marks=td.skip_if_no("pyarrow")),
+    ],
+)
+@pytest.mark.parametrize("cond_type", [["series", "list", "numpy"]])
+def test_where_na(dtype, cond_type):
+    series = Series([None, 1, 2, None, 3, 4, None], dtype=dtype)
+    expected = Series([None, 1, 2, None, -99, -99, None], dtype=dtype)
+    cond = series <= 2
+
+    if cond_type == "list":
+        cond = cond.to_list()
+    elif cond_type == "numpy":
+        cond = cond.to_numpy()
+
+    result = series.where(cond, -99)
+    tm.assert_series_equal(result, expected)