diff --git a/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/filestructurefinder/TimeoutChecker.java b/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/filestructurefinder/TimeoutChecker.java
index a943e7b7a73..99ce19e3ad1 100644
--- a/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/filestructurefinder/TimeoutChecker.java
+++ b/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/filestructurefinder/TimeoutChecker.java
@@ -84,7 +84,6 @@ public class TimeoutChecker implements Closeable {
      * @throws ElasticsearchTimeoutException If the operation is found to have taken longer than the permitted time.
      */
     public void check(String where) {
-
         if (timeoutExceeded) {
             throw new ElasticsearchTimeoutException("Aborting " + operation + " during [" + where +
                 "] as it has taken longer than the timeout of [" + timeout + "]");
@@ -101,7 +100,6 @@ public class TimeoutChecker implements Closeable {
      * @throws ElasticsearchTimeoutException If the operation is found to have taken longer than the permitted time.
      */
     public Map<String, Object> grokCaptures(Grok grok, String text, String where) {
-
         try {
             return grok.captures(text);
         } finally {
@@ -137,12 +135,15 @@ public class TimeoutChecker implements Closeable {
         }
 
         @Override
-        public void register(Matcher matcher) {
+        public synchronized void register(Matcher matcher) {
             WatchDogEntry value = registry.get(Thread.currentThread());
             if (value != null) {
                 boolean wasFalse = value.registered.compareAndSet(false, true);
                 assert wasFalse;
                 value.matchers.add(matcher);
+                if (value.isTimedOut()) {
+                    matcher.interrupt();
+                }
             }
         }
 
@@ -167,8 +168,9 @@ public class TimeoutChecker implements Closeable {
             assert previousValue != null;
         }
 
-        void interruptLongRunningThreadIfRegistered(Thread thread) {
+        synchronized void interruptLongRunningThreadIfRegistered(Thread thread) {
             WatchDogEntry value = registry.get(thread);
+            value.timedOut();
             if (value.registered.get()) {
                 for (Matcher matcher : value.matchers) {
                     matcher.interrupt();
@@ -181,12 +183,21 @@ public class TimeoutChecker implements Closeable {
             final TimeValue timeout;
             final AtomicBoolean registered;
             final Collection<Matcher> matchers;
+            boolean timedOut;
 
             WatchDogEntry(TimeValue timeout) {
                 this.timeout = timeout;
                 this.registered = new AtomicBoolean(false);
                 this.matchers = new CopyOnWriteArrayList<>();
             }
+
+            private void timedOut() {
+                timedOut = true;
+            }
+
+            private boolean isTimedOut() {
+                return timedOut;
+            }
         }
     }
 }
diff --git a/x-pack/plugin/ml/src/test/java/org/elasticsearch/xpack/ml/filestructurefinder/TimeoutCheckerTests.java b/x-pack/plugin/ml/src/test/java/org/elasticsearch/xpack/ml/filestructurefinder/TimeoutCheckerTests.java
index 34c9a047a99..2666bcc44f5 100644
--- a/x-pack/plugin/ml/src/test/java/org/elasticsearch/xpack/ml/filestructurefinder/TimeoutCheckerTests.java
+++ b/x-pack/plugin/ml/src/test/java/org/elasticsearch/xpack/ml/filestructurefinder/TimeoutCheckerTests.java
@@ -59,21 +59,19 @@ public class TimeoutCheckerTests extends FileStructureTestCase {
         }
     }
 
-    @AwaitsFix(bugUrl = "https://github.com/elastic/elasticsearch/issues/48861")
     public void testWatchdog() throws Exception {
-        TimeValue timeout = TimeValue.timeValueMillis(500);
+        final TimeValue timeout = TimeValue.timeValueMillis(randomIntBetween(10, 500));
         try (TimeoutChecker timeoutChecker = new TimeoutChecker("watchdog test", timeout, scheduler)) {
-            TimeoutChecker.TimeoutCheckerWatchdog watchdog = (TimeoutChecker.TimeoutCheckerWatchdog) TimeoutChecker.watchdog;
-
+            final TimeoutChecker.TimeoutCheckerWatchdog watchdog = (TimeoutChecker.TimeoutCheckerWatchdog) TimeoutChecker.watchdog;
             Matcher matcher = mock(Matcher.class);
-            TimeoutChecker.watchdog.register(matcher);
+            watchdog.register(matcher);
             assertThat(watchdog.registry.get(Thread.currentThread()).matchers.size(), equalTo(1));
             try {
                 assertBusy(() -> {
                     verify(matcher).interrupt();
                 });
             } finally {
-                TimeoutChecker.watchdog.unregister(matcher);
+                watchdog.unregister(matcher);
                 assertThat(watchdog.registry.get(Thread.currentThread()).matchers.size(), equalTo(0));
             }
         }