@@ -131,6 +131,7 @@ class IndexFile(LazyMixin, git_diff.Diffable, Serializable):
     """
 
     unsafe_git_checkout_index_options = ["--prefix"]
+    unsafe_git_read_tree_options = ["--index-output"]
 
     __slots__ = ("repo", "version", "entries", "_extension_data", "_file_path")
 
@@ -256,7 +257,12 @@ def write(
 
     @post_clear_cache
     @default_index
-    def merge_tree(self, rhs: Treeish, base: Union[None, Treeish] = None) -> "IndexFile":
+    def merge_tree(
+        self,
+        rhs: Treeish,
+        base: Union[None, Treeish] = None,
+        allow_unsafe_options: bool = False,
+    ) -> "IndexFile":
         """Merge the given `rhs` treeish into the current index, possibly taking
         a common base treeish into account.
 
@@ -270,6 +276,9 @@ def merge_tree(self, rhs: Treeish, base: Union[None, Treeish] = None) -> "IndexF
             Optional treeish reference pointing to the common base of `rhs` and this
             index which equals lhs.
 
+        :param allow_unsafe_options:
+            Allow options that may write to arbitrary paths.
+
         :return:
             self (containing the merge and possibly unmerged entries in case of
             conflicts)
@@ -280,6 +289,12 @@ def merge_tree(self, rhs: Treeish, base: Union[None, Treeish] = None) -> "IndexF
             yourself, you have to commit the changed index (or make a valid tree from
             it) and retry with a three-way :meth:`index.from_tree <from_tree>` call.
         """
+        if not allow_unsafe_options:
+            Git.check_unsafe_options(
+                options=Git._option_candidates([base, rhs]),
+                unsafe_options=self.unsafe_git_read_tree_options,
+            )
+
         # -i : ignore working tree status
         # --aggressive : handle more merge cases
         # -m : do an actual merge
@@ -324,7 +339,13 @@ def new(cls, repo: "Repo", *tree_sha: Union[str, Tree]) -> "IndexFile":
         return inst
 
     @classmethod
-    def from_tree(cls, repo: "Repo", *treeish: Treeish, **kwargs: Any) -> "IndexFile":
+    def from_tree(
+        cls,
+        repo: "Repo",
+        *treeish: Treeish,
+        allow_unsafe_options: bool = False,
+        **kwargs: Any,
+    ) -> "IndexFile":
         R"""Merge the given treeish revisions into a new index which is returned.
         The original index will remain unaltered.
 
@@ -348,6 +369,9 @@ def from_tree(cls, repo: "Repo", *treeish: Treeish, **kwargs: Any) -> "IndexFile
         :param kwargs:
             Additional arguments passed to :manpage:`git-read-tree(1)`.
 
+        :param allow_unsafe_options:
+            Allow options that may write to arbitrary paths.
+
         :return:
             New :class:`IndexFile` instance. It will point to a temporary index location
             which does not exist anymore. If you intend to write such a merged Index,
@@ -365,6 +389,12 @@ def from_tree(cls, repo: "Repo", *treeish: Treeish, **kwargs: Any) -> "IndexFile
         if len(treeish) == 0 or len(treeish) > 3:
             raise ValueError("Please specify between 1 and 3 treeish, got %i" % len(treeish))
 
+        if not allow_unsafe_options:
+            Git.check_unsafe_options(
+                options=Git._option_candidates(treeish, kwargs),
+                unsafe_options=cls.unsafe_git_read_tree_options,
+            )
+
         arg_list: List[Union[Treeish, str]] = []
         # Ignore that the working tree and index possibly are out of date.
         if len(treeish) > 1:
@@ -1414,6 +1444,7 @@ def reset(
         working_tree: bool = False,
         paths: Union[None, Iterable[PathLike]] = None,
         head: bool = False,
+        allow_unsafe_options: bool = False,
         **kwargs: Any,
     ) -> "IndexFile":
         """Reset the index to reflect the tree at the given commit. This will not adjust
@@ -1445,6 +1476,9 @@ def reset(
             The paths need to exist at the commit, otherwise an exception will be
             raised.
 
+        :param allow_unsafe_options:
+            Allow options that may write to arbitrary paths.
+
         :param kwargs:
             Additional keyword arguments passed to :manpage:`git-reset(1)`.
 
@@ -1461,7 +1495,7 @@ def reset(
         """
         # What we actually want to do is to merge the tree into our existing index,
         # which is what git-read-tree does.
-        new_inst = type(self).from_tree(self.repo, commit)
+        new_inst = type(self).from_tree(self.repo, commit, allow_unsafe_options=allow_unsafe_options)
         if not paths:
             self.entries = new_inst.entries
         else:
 
@@ -327,6 +327,22 @@ def add_bad_blob():
         except Exception as ex:
             assert "index.lock' could not be obtained" not in str(ex)
 
+    @with_rw_repo("0.1.6")
+    def test_read_tree_methods_reject_index_output(self, rw_repo):
+        output_path = (Path(rw_repo.working_tree_dir) / "alternate-index").as_posix()
+        unsafe_option = f"--index-output={output_path}"
+
+        with pytest.raises(UnsafeOptionError):
+            IndexFile.from_tree(rw_repo, unsafe_option)
+        with pytest.raises(UnsafeOptionError):
+            IndexFile.from_tree(rw_repo, "HEAD", index_output=output_path)
+        with pytest.raises(UnsafeOptionError):
+            rw_repo.index.reset(unsafe_option)
+        with pytest.raises(UnsafeOptionError):
+            rw_repo.index.merge_tree(unsafe_option)
+        with pytest.raises(UnsafeOptionError):
+            rw_repo.index.merge_tree("HEAD", base=unsafe_option)
+
     @with_rw_repo("0.1.6")
     def test_index_file_from_tree(self, rw_repo):
         common_ancestor_sha = "5117c9c8a4d3af19a9958677e45cda9269de1541"