diff --git a/doc/source/whatsnew/v3.0.0.rst b/doc/source/whatsnew/v3.0.0.rst
index 0df5a70d87655..2900db24a99ff 100644
--- a/doc/source/whatsnew/v3.0.0.rst
+++ b/doc/source/whatsnew/v3.0.0.rst
@@ -712,7 +712,7 @@ MultiIndex
 - :func:`MultiIndex.get_level_values` accessing a :class:`DatetimeIndex` does not carry the frequency attribute along (:issue:`58327`, :issue:`57949`)
 - Bug in :class:`DataFrame` arithmetic operations in case of unaligned MultiIndex columns (:issue:`60498`)
 - Bug in :class:`DataFrame` arithmetic operations with :class:`Series` in case of unaligned MultiIndex (:issue:`61009`)
--
+- Bug in :meth:`MultiIndex.from_tuples` causing wrong output with input of type tuples having NaN values (:issue:`60695`, :issue:`60988`)
 
 I/O
 ^^^
diff --git a/pandas/core/algorithms.py b/pandas/core/algorithms.py
index aafd802b827a5..0c0232bdc6d4c 100644
--- a/pandas/core/algorithms.py
+++ b/pandas/core/algorithms.py
@@ -1647,6 +1647,8 @@ def map_array(
         If the function returns a tuple with more than one element
         a MultiIndex will be returned.
     """
+    from pandas import Index
+
     if na_action not in (None, "ignore"):
         msg = f"na_action must either be 'ignore' or None, {na_action} was passed"
         raise ValueError(msg)
@@ -1676,6 +1678,10 @@ def map_array(
 
             if len(mapper) == 0:
                 mapper = Series(mapper, dtype=np.float64)
+            elif isinstance(mapper, dict):
+                mapper = Series(
+                    mapper.values(), index=Index(mapper.keys(), tupleize_cols=False)
+                )
             else:
                 mapper = Series(mapper)
 
diff --git a/pandas/core/indexes/multi.py b/pandas/core/indexes/multi.py
index 79eb1b693d866..29b34f560ab2e 100644
--- a/pandas/core/indexes/multi.py
+++ b/pandas/core/indexes/multi.py
@@ -9,6 +9,7 @@
     Sequence,
 )
 from functools import wraps
+from itertools import zip_longest
 from sys import getsizeof
 from typing import (
     TYPE_CHECKING,
@@ -588,7 +589,7 @@ def from_tuples(
         elif isinstance(tuples, list):
             arrays = list(lib.to_object_array_tuples(tuples).T)
         else:
-            arrs = zip(*tuples)
+            arrs = zip_longest(*tuples, fillvalue=np.nan)
             arrays = cast(list[Sequence[Hashable]], arrs)
 
         return cls.from_arrays(arrays, sortorder=sortorder, names=names)
diff --git a/pandas/tests/indexes/multi/test_constructors.py b/pandas/tests/indexes/multi/test_constructors.py
index b2867d4ac8e68..92827cf154394 100644
--- a/pandas/tests/indexes/multi/test_constructors.py
+++ b/pandas/tests/indexes/multi/test_constructors.py
@@ -410,6 +410,19 @@ def test_from_tuples_with_tuple_label():
     tm.assert_frame_equal(expected, result)
 
 
+@pytest.mark.parametrize(
+    "keys, expected",
+    [
+        ((("l1",), ("l1", "l2")), (("l1", np.nan), ("l1", "l2"))),
+        ((("l1", "l2"), ("l1",)), (("l1", "l2"), ("l1", np.nan))),
+    ],
+)
+def test_from_tuples_with_various_tuple_lengths(keys, expected):
+    # GH 60695
+    idx = MultiIndex.from_tuples(keys)
+    assert tuple(idx) == expected
+
+
 # ----------------------------------------------------------------------------
 # from_product
 # ----------------------------------------------------------------------------
diff --git a/pandas/tests/series/test_constructors.py b/pandas/tests/series/test_constructors.py
index a2be698c0ec28..5f4a100e7ccc7 100644
--- a/pandas/tests/series/test_constructors.py
+++ b/pandas/tests/series/test_constructors.py
@@ -1441,10 +1441,17 @@ def test_constructor_tuple_of_tuples(self):
         s = Series(data)
         assert tuple(s) == data
 
-    def test_constructor_dict_of_tuples(self):
-        data = {(1, 2): 3, (None, 5): 6}
+    @pytest.mark.parametrize(
+        "data, expected_values, expected_index",
+        [
+            ({(1, 2): 3, (None, 5): 6}, [3, 6], [(1, 2), (None, 5)]),
+            ({(1,): 3, (4, 5): 6}, [3, 6], [(1, None), (4, 5)]),
+        ],
+    )
+    def test_constructor_dict_of_tuples(self, data, expected_values, expected_index):
+        # GH 60695
         result = Series(data).sort_values()
-        expected = Series([3, 6], index=MultiIndex.from_tuples([(1, 2), (None, 5)]))
+        expected = Series(expected_values, index=MultiIndex.from_tuples(expected_index))
         tm.assert_series_equal(result, expected)
 
     # https://github.com/pandas-dev/pandas/issues/22698
@@ -1860,23 +1867,30 @@ class A(OrderedDict):
         series = Series(A(data))
         tm.assert_series_equal(series, expected)
 
-    def test_constructor_dict_multiindex(self):
-        d = {("a", "a"): 0.0, ("b", "a"): 1.0, ("b", "c"): 2.0}
-        _d = sorted(d.items())
-        result = Series(d)
-        expected = Series(
-            [x[1] for x in _d], index=MultiIndex.from_tuples([x[0] for x in _d])
-        )
-        tm.assert_series_equal(result, expected)
+    @pytest.mark.parametrize(
+        "data, expected_index_multi",
+        [
+            ({("a", "a"): 0.0, ("b", "a"): 1.0, ("b", "c"): 2.0}, True),
+            ({("a",): 0.0, ("a", "b"): 1.0}, True),
+            ({"z": 111.0, ("a", "a"): 0.0, ("b", "a"): 1.0, ("b", "c"): 2.0}, False),
+        ],
+    )
+    def test_constructor_dict_multiindex(self, data, expected_index_multi):
+        # GH#60695
+        result = Series(data)
 
-        d["z"] = 111.0
-        _d.insert(0, ("z", d["z"]))
-        result = Series(d)
-        expected = Series(
-            [x[1] for x in _d], index=Index([x[0] for x in _d], tupleize_cols=False)
-        )
-        result = result.reindex(index=expected.index)
-        tm.assert_series_equal(result, expected)
+        if expected_index_multi:
+            expected = Series(
+                list(data.values()),
+                index=MultiIndex.from_tuples(list(data.keys())),
+            )
+            tm.assert_series_equal(result, expected)
+        else:
+            expected = Series(
+                list(data.values()),
+                index=Index(list(data.keys())),
+            )
+            tm.assert_series_equal(result, expected)
 
     def test_constructor_dict_multiindex_reindex_flat(self):
         # construction involves reindexing with a MultiIndex corner case