diff --git a/meta/recipes-devtools/apt/apt-native.inc b/meta/recipes-devtools/apt/apt-native.inc
index ab89f71..ae03f6e 100644
--- a/meta/recipes-devtools/apt/apt-native.inc
+++ b/meta/recipes-devtools/apt/apt-native.inc
@@ -20,11 +20,13 @@ python do_install_config () {
 
     data = d.expand(data)
 
-    outdir = os.path.join(d.getVar('D', True), d.getVar('sysconfdir', True), 'apt')
+    # os.path.join does not allow sysconfdir to be a absolute dir
+    outdir = os.path.join(d.getVar('D', True), d.getVar('sysconfdir', True)[1:], 'apt')
     if not os.path.exists(outdir):
         os.makedirs(outdir)
-        outpath = os.path.join(outdir, 'apt.conf.sample')
 
+    outpath = os.path.join(outdir, 'apt.conf.sample')
+    if not os.path.exists(outpath):
         outfile = file(outpath, 'w')
         outfile.write(data)
         outfile.close()