diff --git a/pyext/setup.py.in b/pyext/setup.py.in
index 6ac7ebb..3d53a7f 100644
--- a/pyext/setup.py.in
+++ b/pyext/setup.py.in
@@ -53,9 +53,13 @@ except:
 # Set default include directories and data files
 include_dirs = ['@prefix@/include/gammalib']
 data_files   = glob.glob('@top_srcdir@/pyext/*.i')
-library_dirs = ['../src/.libs','@prefix@/lib']
+library_dirs = ['../src/.libs']
 libraries    = [libcta,'gamma']
 
+# Append prefix library directory if it exists
+if os.path.exists('@prefix@/lib'):
+	library_dirs.append(['@prefix@/lib'])
+
 # Add application include files. The method we use here is not very
 # intelligent as it simple will add all names that start with 'ct'
 # in the src directory. Once we added the ctatools script we had to
@@ -75,18 +79,18 @@ for extra_lib in extra_libs:
 # Get extra library paths
 extra_lib_paths = ('@LDFLAGS@').split(' ')
 for extra_lib_path in extra_lib_paths:
-	if extra_lib_path.lstrip().find('-L') == 0:
+	if extra_lib_path.lstrip().find('-L') != -1:
 		dir = extra_lib_path.lstrip().lstrip('-L')
 		if len(dir) > 0:
-			library_dirs.append(extra_lib_path.lstrip('-L'))
+			library_dirs.append(dir)
 
 # Get extra include directories
 extra_include_dirs = ('@CPPFLAGS@').split(' ')
 for extra_include_dir in extra_include_dirs:
-	if extra_include_dir.lstrip().find('-I') == 0:
+	if extra_include_dir.lstrip().find('-I') != -1:
 		dir = extra_include_dir.lstrip().lstrip('-I')
 		if len(dir) > 0:
-			include_dirs.append(extra_include_dir.lstrip('-I'))
+			include_dirs.append(dir)
 
 # Setup
 setup(name='@PACKAGE_NAME@',