diff --git a/aclocal.in b/aclocal.in
index b51c09d..29be10e 100644
--- a/aclocal.in
+++ b/aclocal.in
@@ -165,6 +165,11 @@ my @ac_config_macro_dirs;
 # If set, names a temporary file that must be erased on abnormal exit.
 my $erase_me;
 
+# constants for scan_m4_dirs($ERR_LEVEL) parameter
+use constant SCAN_M4_DIRS_SILENT => 0;
+use constant SCAN_M4_DIRS_WARN => 1;
+use constant SCAN_M4_DIRS_ERROR => 2;
+
 ################################################################
 
 # Prototypes for all subroutines.
@@ -355,21 +360,29 @@ sub list_compare (\@\@)
 
 ################################################################
 
-# scan_m4_dirs($TYPE, $ERR_ON_NONEXISTING, @DIRS)
+# scan_m4_dirs($TYPE, $ERR_LEVEL, @DIRS)
 # -----------------------------------------------
 # Scan all M4 files installed in @DIRS for new macro definitions.
 # Register each file as of type $TYPE (one of the FT_* constants).
+# Fail without discussion on non-existing include directory when the
+# $ERR_LEVEL parameter equals to SCAN_M4_DIRS_ERROR, just print warning
+# when it equals to SCAN_M4_DIRS_WARN and don't complain at all when
+# it is set to SCAN_M4_DIRS_SILENT.
 sub scan_m4_dirs ($$@)
 {
-  my ($type, $err_on_nonexisting, @dirlist) = @_;
+  my ($type, $err_level, @dirlist) = @_;
 
   foreach my $m4dir (@dirlist)
     {
       if (! opendir (DIR, $m4dir))
 	{
 	  # TODO: maybe avoid complaining only if errno == ENONENT?
-	  next unless $err_on_nonexisting;
-	  fatal "couldn't open directory '$m4dir': $!";
+	  my $message = "couldn't open directory '$m4dir': $!";
+
+	  fatal $message if $err_level == SCAN_M4_DIRS_ERROR;
+	  msg ('unsupported', $message) if $err_level == SCAN_M4_DIRS_WARN;
+	  # don't complain if $err_level == SCAN_M4_DIRS_SILENT
+	  next
 	}
 
       # We reverse the directory contents so that foo2.m4 gets
@@ -406,13 +419,25 @@ sub scan_m4_files ()
 
   if (@user_includes)
     {
+      # Don't explore the same directory multiple times.  This is here not
+      # only for speedup purposes.  We need this when the user has e.g.
+      # specified 'ACLOCAL_AMFLAGS = -I m4' and has also set
+      # AC_CONFIG_MACRO_DIR[S]([m4]) in configure.ac.  This makes the 'm4'
+      # directory to occur twice here and fail on the second call to
+      # scan_m4_dirs([m4]) when the 'm4' directory doesn't exist.
+      # TODO: Shouldn't there be rather a check in scan_m4_dirs for
+      #       @user_includes[0]?
+      @user_includes = uniq @user_includes;
+
       # Don't complain if the first user directory doesn't exist, in case
       # we need to create it later (can happen if '--install' was given).
-      scan_m4_dirs (FT_USER, !$install, $user_includes[0]);
-      scan_m4_dirs (FT_USER, 1, @user_includes[1..$#user_includes]);
+      my $first_dir_lvl = $install ? SCAN_M4_DIRS_SILENT : SCAN_M4_DIRS_WARN;
+      scan_m4_dirs (FT_USER, $first_dir_lvl, $user_includes[0]);
+      scan_m4_dirs (FT_USER, SCAN_M4_DIRS_ERROR,
+		    @user_includes[1..$#user_includes]);
     }
-  scan_m4_dirs (FT_AUTOMAKE, 1, @automake_includes);
-  scan_m4_dirs (FT_SYSTEM,   1, @system_includes);
+  scan_m4_dirs (FT_AUTOMAKE, SCAN_M4_DIRS_ERROR, @automake_includes);
+  scan_m4_dirs (FT_SYSTEM, SCAN_M4_DIRS_ERROR, @system_includes);
 
   # Construct a new function that does the searching.  We use a
   # function (instead of just evaluating $search in the loop) so that
diff --git a/t/aclocal-macrodir.tap b/t/aclocal-macrodir.tap
index 3c66e53..bdeb30d 100755
--- a/t/aclocal-macrodir.tap
+++ b/t/aclocal-macrodir.tap
@@ -20,7 +20,7 @@
 am_create_testdir=empty
 . test-init.sh
 
-plan_ 6
+plan_ 7
 
 ocwd=$(pwd) || fatal_ "getting current working directory"
 ACLOCAL_PATH=; unset ACLOCAL_PATH
@@ -105,7 +105,9 @@ mkdir sys-dir the-dir
 echo 'AC_DEFUN([THE_MACRO], [:])' > sys-dir/my.m4
 
 test ! -r the-dir/my.m4 \
-  && $ACLOCAL --install --system-acdir ./sys-dir \
+  && $ACLOCAL --install --system-acdir ./sys-dir 2>stderr \
+  && cat stderr >&2 \
+  && not grep "couldn't open directory" stderr \
   && diff sys-dir/my.m4 the-dir/my.m4 \
   || r='not ok'
 
@@ -149,7 +151,9 @@ mkdir acdir
 echo 'AC_DEFUN([MY_MACRO], [:])' > acdir/bar.m4
 
 test ! -d foo \
-  && $ACLOCAL --install --system-acdir ./acdir \
+  && $ACLOCAL --install --system-acdir ./acdir 2>stderr \
+  && cat stderr >&2 \
+  && not grep "couldn't open directory" stderr \
   && diff acdir/bar.m4 foo/bar.m4 \
   || r='not ok'
 
@@ -157,14 +161,14 @@ test_end
 
 #---------------------------------------------------------------------------
 
-test_begin "AC_CONFIG_MACRO_DIR([non-existent]) errors out (1)"
+test_begin "AC_CONFIG_MACRO_DIR([non-existent]) warns but succeeds"
 
 cat > configure.ac << 'END'
 AC_INIT([oops], [1.0])
 AC_CONFIG_MACRO_DIR([non-existent])
 END
 
-not $ACLOCAL -Wnone 2>stderr \
+$ACLOCAL -Wno-error 2>stderr \
   && cat stderr >&2 \
   && grep "couldn't open directory 'non-existent'" stderr \
   || r='not ok'
@@ -173,6 +177,26 @@ test_end
 
 #---------------------------------------------------------------------------
 
+test_begin "AC_CONFIG_MACRO_DIR([not-exist]) and ACLOCAL_AMFLAGS = -I not-exist"
+
+cat > configure.ac << 'END'
+AC_INIT([oops], [1.0])
+AC_CONFIG_MACRO_DIR([not-exist])
+END
+
+cat > Makefile.am << 'END'
+ACLOCAL_AMFLAGS = -I not-exist
+END
+
+$ACLOCAL -Wno-error 2>stderr \
+  && cat stderr >&2 \
+  && grep "couldn't open directory 'not-exist'" stderr \
+  || r='not ok'
+
+test_end
+
+#---------------------------------------------------------------------------
+
 # Avoid spurious failures with pre-2.70 autoconf.
 # FIXME: remove this in automake 1.14, once we require Autoconf 2.70.
 if echo 'AC_INIT AC_CONFIG_MACRO_DIRS' | $AUTOCONF -o/dev/null -; then