diff --git a/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/CLIText.properties b/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/CLIText.properties
index eed05e89f..07d9c00c7 100644
--- a/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/CLIText.properties
+++ b/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/CLIText.properties
@@ -65,7 +65,9 @@ jgitVersion=jgit version {0}
 lineFormat=# {0}
 listeningOn=Listening on {0}
 mergeConflict=CONFLICT(content): Merge conflict in {0}
+mergeCheckoutConflict=error: Your local changes to the following files would be overwritten by merge:
 mergeFailed=Automatic merge failed; fix conflicts and then commit the result
+mergeCheckoutFailed=Please, commit your changes or stash them before you can merge.
 mergeMadeBy=Merge made by the ''{0}'' strategy.
 mergedSquashed=Squash commit -- not updating HEAD\nAutomatic merge went well; stopped before committing as requested
 mergeWentWellStoppedBeforeCommitting=Automatic merge went well; stopped before committing as requested
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CLIText.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CLIText.java
index 64bd18e86..1f14fa272 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CLIText.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/CLIText.java
@@ -133,8 +133,10 @@ public class CLIText extends TranslationBundle {
 	/***/ public String jgitVersion;
 	/***/ public String lineFormat;
 	/***/ public String listeningOn;
+	/***/ public String mergeCheckoutConflict;
 	/***/ public String mergeConflict;
 	/***/ public String mergeFailed;
+	/***/ public String mergeCheckoutFailed;
 	/***/ public String mergeMadeBy;
 	/***/ public String mergedSquashed;
 	/***/ public String mergeWentWellStoppedBeforeCommitting;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java
index 97198259d..e25ac4f3e 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Merge.java
@@ -51,6 +51,7 @@ import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.MergeCommand;
 import org.eclipse.jgit.api.MergeResult;
 import org.eclipse.jgit.api.MergeCommand.FastForwardMode;
+import org.eclipse.jgit.api.errors.CheckoutConflictException;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
@@ -119,7 +120,12 @@ class Merge extends TextBuiltin {
 			mergeCmd.include(srcRef);
 		else
 			mergeCmd.include(src);
-		MergeResult result = mergeCmd.call();
+		MergeResult result;
+		try {
+			result = mergeCmd.call();
+		} catch (CheckoutConflictException e) {
+			result = new MergeResult(e.getConflictingPaths()); // CHECKOUT_CONFLICT
+		}
 
 		switch (result.getMergeStatus()) {
 		case ALREADY_UP_TO_DATE:
@@ -134,6 +140,12 @@ class Merge extends TextBuiltin {
 					.name()));
 			outw.println(result.getMergeStatus().toString());
 			break;
+		case CHECKOUT_CONFLICT:
+			outw.println(CLIText.get().mergeCheckoutConflict);
+			for (String collidingPath : result.getCheckoutConflicts())
+				outw.println("\t" + collidingPath); //$NON-NLS-1$
+			outw.println(CLIText.get().mergeCheckoutFailed);
+			break;
 		case CONFLICTING:
 			for (String collidingPath : result.getConflicts().keySet())
 				outw.println(MessageFormat.format(CLIText.get().mergeConflict,