diff --git a/tools/lint/common.c b/tools/lint/common.c
index fc9b1cd..f177527 100644
--- a/tools/lint/common.c
+++ b/tools/lint/common.c
@@ -755,7 +755,7 @@
 
     if (merge) {
         /* validate the merged result */
-        ret = lyd_validate_all(&merged_tree, ctx, LYD_VALIDATE_PRESENT, NULL);
+        ret = lyd_validate_all(&merged_tree, ctx, options_validate, NULL);
         if (ret) {
             YLMSG_E("Merged data are not valid.\n");
             goto cleanup;
diff --git a/tools/lint/tests/interactive/data_present.test b/tools/lint/tests/interactive/data_present.test
index 4228fa6..4bba596 100644
--- a/tools/lint/tests/interactive/data_present.test
+++ b/tools/lint/tests/interactive/data_present.test
@@ -9,6 +9,13 @@
     ly_cmd "data -e $ddir/modleaf.xml"
 }}
 
+test data_present_merge {validation with --present and --merge} {
+-setup $ly_setup -cleanup $ly_cleanup -body {
+    ly_cmd "load modleaf modmandatory moddefault"
+    ly_cmd_err "data -m $ddir/modleaf.xml $ddir/moddefault.xml" "Mandatory node \"lft\" instance does not exist."
+    ly_cmd "data -e -m $ddir/modleaf.xml $ddir/moddefault.xml"
+}}
+
 test data_present_merge_invalid {using --present and --merge but data are invalid} {
 -setup $ly_setup -cleanup $ly_cleanup -body {
     ly_cmd "load modleaf modmandatory"
diff --git a/tools/lint/tests/non-interactive/data_present.test b/tools/lint/tests/non-interactive/data_present.test
index 5ff8783..81aac14 100644
--- a/tools/lint/tests/non-interactive/data_present.test
+++ b/tools/lint/tests/non-interactive/data_present.test
@@ -9,6 +9,13 @@
     ly_cmd "-e $ddir/modleaf.xml $mods"
 } {}
 
+test data_present_merge {validation with --present and --merge} {
+    set mods "$mdir/modleaf.yang $mdir/modmandatory.yang $mdir/moddefault.yang"
+    set data "$ddir/modleaf.xml $ddir/moddefault.xml"
+    ly_cmd_err "-m $data $mods" "Mandatory node \"lft\" instance does not exist."
+    ly_cmd "-m -e $data $mods"
+} {}
+
 test data_present_merge_invalid {using --present and --merge but data are invalid} {
     set mods "$mdir/modleaf.yang $mdir/modmandatory.yang"
     set data "$ddir/modleaf.xml $ddir/modmandatory_invalid.xml"