diff --git a/tools/export/makefile/__init__.py b/tools/export/makefile/__init__.py
index cab92260f9..c26c45bc07 100644
--- a/tools/export/makefile/__init__.py
+++ b/tools/export/makefile/__init__.py
@@ -228,9 +228,10 @@ class Arm(Makefile):
 
     def generate(self):
         if self.resources.linker_script:
+            sct_file = self.resources.linker_script
             new_script = self.toolchain.correct_scatter_shebang(
-                self.resources.linker_script)
-            if new_script is not self.resources.linker_script:
+                sct_file, join(self.resources.file_basepath[sct_file], "BUILD"))
+            if new_script is not sct_file:
                 self.resources.linker_script = new_script
                 self.generated_files.append(new_script)
         return super(Arm, self).generate()
diff --git a/tools/export/uvision/__init__.py b/tools/export/uvision/__init__.py
index 8382bae0f0..683c9fab12 100644
--- a/tools/export/uvision/__init__.py
+++ b/tools/export/uvision/__init__.py
@@ -217,12 +217,14 @@ class Uvision(Exporter):
             # UVFile tuples defined above
             'project_files': sorted(list(self.format_src(srcs).iteritems()),
                                     key=lambda (group, _): group.lower()),
-            'linker_script':self.toolchain.correct_scatter_shebang(
-                self.resources.linker_script),
             'include_paths': '; '.join(self.resources.inc_dirs).encode('utf-8'),
             'device': DeviceUvision(self.target),
         }
-        self.generated_files.append(ctx['linker_script'])
+        sct_file = self.resources.linker_script
+        ctx['linker_script'] = self.toolchain.correct_scatter_shebang(
+            sct_file, self.resources.file_basepath[sct_file])
+        if ctx['linker_script'] != sct_file:
+            self.generated_files.append(ctx['linker_script'])
         core = ctx['device'].core
         ctx['cputype'] = core.rstrip("FD")
         if core.endswith("FD"):
diff --git a/tools/toolchains/arm.py b/tools/toolchains/arm.py
index 7941ede65e..a6c91c4cfe 100644
--- a/tools/toolchains/arm.py
+++ b/tools/toolchains/arm.py
@@ -16,8 +16,8 @@ limitations under the License.
 """
 import re
 from copy import copy
-from os.path import join, dirname, splitext, basename, exists
-from os import makedirs, write
+from os.path import join, dirname, splitext, basename, exists, relpath
+from os import makedirs, write, curdir
 from tempfile import mkstemp
 
 from tools.toolchains import mbedToolchain, TOOLCHAIN_PATHS
@@ -184,7 +184,7 @@ class ARM(mbedToolchain):
     def compile_cpp(self, source, object, includes):
         return self.compile(self.cppc, source, object, includes)
 
-    def correct_scatter_shebang(self, scatter_file):
+    def correct_scatter_shebang(self, scatter_file, base_path=curdir):
         """Correct the shebang at the top of a scatter file.
 
         Positional arguments:
@@ -203,7 +203,8 @@ class ARM(mbedToolchain):
                 return scatter_file
             else:
                 new_scatter = join(self.build_dir, ".link_script.sct")
-                self.SHEBANG += " -I %s" % dirname(scatter_file)
+                self.SHEBANG += " -I %s" % relpath(dirname(scatter_file),
+                                                   base_path)
                 if self.need_update(new_scatter, [scatter_file]):
                     with open(new_scatter, "wb") as out:
                         out.write(self.SHEBANG)