diff --git a/mesonbuild/backend/ninjabackend.py b/mesonbuild/backend/ninjabackend.py
index a3b9ce8b2..405bd26cd 100644
--- a/mesonbuild/backend/ninjabackend.py
+++ b/mesonbuild/backend/ninjabackend.py
@@ -1757,7 +1757,7 @@ rule FORTRAN_DEP_HACK%s
         exe_arr = self.exe_object_to_cmd_array(exe)
         infilelist = genlist.get_inputs()
         outfilelist = genlist.get_outputs()
-        extra_dependencies = [os.path.join(self.build_to_src, i) for i in genlist.extra_depends]
+        extra_dependencies = self.get_custom_target_depend_files(genlist)
         for i in range(len(infilelist)):
             curfile = infilelist[i]
             if len(generator.outputs) == 1:
diff --git a/mesonbuild/build.py b/mesonbuild/build.py
index dae94b6ed..66f08d818 100644
--- a/mesonbuild/build.py
+++ b/mesonbuild/build.py
@@ -1365,8 +1365,17 @@ class GeneratedList:
         self.outfilelist = []
         self.outmap = {}
         self.extra_depends = []
+        self.depend_files = []
         self.preserve_path_from = preserve_path_from
         self.extra_args = extra_args
+        if isinstance(generator.exe, dependencies.ExternalProgram):
+            if not generator.exe.found():
+                raise InvalidArguments('Tried to use not-found external program as generator')
+            path = generator.exe.get_path()
+            if os.path.isabs(path):
+                # Can only add a dependency on an external program which we
+                # know the absolute path of
+                self.depend_files.append(File.from_absolute_file(path))
 
     def add_preserved_path_segment(self, infile, outfiles, state):
         result = []
@@ -1962,8 +1971,7 @@ class CustomTarget(Target):
                 final_cmd.append(c)
             elif isinstance(c, dependencies.ExternalProgram):
                 if not c.found():
-                    m = 'Tried to use not-found external program {!r} in "command"'
-                    raise InvalidArguments(m.format(c.name))
+                    raise InvalidArguments('Tried to use not-found external program in "command"')
                 path = c.get_path()
                 if os.path.isabs(path):
                     # Can only add a dependency on an external program which we