diff --git a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/logging/DataflowWorkerLoggingInitializer.java b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/logging/DataflowWorkerLoggingInitializer.java
index 56688470dc79..ebef8ea707cd 100644
--- a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/logging/DataflowWorkerLoggingInitializer.java
+++ b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/logging/DataflowWorkerLoggingInitializer.java
@@ -29,6 +29,7 @@
 import java.io.PrintStream;
 import java.util.List;
 import java.util.Map;
+import java.util.logging.ErrorManager;
 import java.util.logging.Level;
 import java.util.logging.LogManager;
 import java.util.logging.Logger;
@@ -98,6 +99,35 @@ public class DataflowWorkerLoggingInitializer {
   private static PrintStream originalStdErr = System.err;
   private static boolean initialized = false;
 
+  // This is the same as ErrorManager except that it uses the provided
+  // print stream.
+  public static class PrintStreamErrorManager extends ErrorManager {
+    public PrintStreamErrorManager(PrintStream stream) {
+      this.stream = stream;
+    }
+
+    private PrintStream stream;
+    private boolean reported = false;
+
+    @Override
+    public synchronized void error(String msg, Exception ex, int code) {
+      if (reported) {
+        // We only report the first error, to avoid clogging
+        // the screen.
+        return;
+      }
+      reported = true;
+      String text = "java.util.logging.ErrorManager: " + code;
+      if (msg != null) {
+        text = text + ": " + msg;
+      }
+      stream.println(text);
+      if (ex != null) {
+        ex.printStackTrace(stream);
+      }
+    }
+  };
+
   private static DataflowWorkerLoggingHandler makeLoggingHandler(
       String filepathProperty, String defaultFilePath) throws IOException {
     String filepath = System.getProperty(filepathProperty, defaultFilePath);
@@ -105,6 +135,9 @@ private static DataflowWorkerLoggingHandler makeLoggingHandler(
     DataflowWorkerLoggingHandler handler =
         new DataflowWorkerLoggingHandler(filepath, filesizeMb * 1024L * 1024L);
     handler.setLevel(Level.ALL);
+    // To avoid potential deadlock between the handler and the System.err print stream, use the
+    // original stderr print stream for errors. See BEAM-9399.
+    handler.setErrorManager(new PrintStreamErrorManager(getOriginalStdErr()));
     return handler;
   }
 
diff --git a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/logging/JulHandlerPrintStreamAdapterFactory.java b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/logging/JulHandlerPrintStreamAdapterFactory.java
index 08a995d8275a..79ef587a89c6 100644
--- a/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/logging/JulHandlerPrintStreamAdapterFactory.java
+++ b/runners/google-cloud-dataflow-java/worker/src/main/java/org/apache/beam/runners/dataflow/worker/logging/JulHandlerPrintStreamAdapterFactory.java
@@ -17,8 +17,6 @@
  */
 package org.apache.beam.runners.dataflow.worker.logging;
 
-import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkState;
-
 import java.io.IOException;
 import java.io.OutputStream;
 import java.io.PrintStream;
@@ -96,10 +94,10 @@ public void write(int i) throws IOException {
 
     @Override
     public void flush() {
-      publishIfNonEmpty(flushToString());
+      publishIfNonEmpty(flushBufferToString());
     }
 
-    private synchronized String flushToString() {
+    private synchronized String flushBufferToString() {
       if (buffer.length() > 0 && buffer.charAt(buffer.length() - 1) == '\n') {
         buffer.setLength(buffer.length() - 1);
       }
@@ -167,7 +165,7 @@ public void write(byte[] a, int offset, int length) {
           int startLength = buffer.length();
           buffer.append(decoded);
           if (flush || buffer.indexOf("\n", startLength) >= 0) {
-            msg = flushToString();
+            msg = flushBufferToString();
           }
         }
       }
@@ -218,7 +216,7 @@ public void print(char[] a) {
         if (!flush) {
           return;
         }
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
     }
@@ -232,7 +230,7 @@ public void print(String s) {
         if (!flush) {
           return;
         }
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
     }
@@ -252,7 +250,7 @@ public void println(boolean b) {
       String msg;
       synchronized (this) {
         buffer.append(b);
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
     }
@@ -262,7 +260,7 @@ public void println(char c) {
       String msg;
       synchronized (this) {
         buffer.append(c);
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
     }
@@ -272,7 +270,7 @@ public void println(int i) {
       String msg;
       synchronized (this) {
         buffer.append(i);
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
     }
@@ -282,7 +280,7 @@ public void println(long l) {
       String msg;
       synchronized (this) {
         buffer.append(l);
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
     }
@@ -292,7 +290,7 @@ public void println(float f) {
       String msg;
       synchronized (this) {
         buffer.append(f);
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
     }
@@ -302,7 +300,7 @@ public void println(double d) {
       String msg;
       synchronized (this) {
         buffer.append(d);
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
     }
@@ -312,7 +310,7 @@ public void println(char[] a) {
       String msg;
       synchronized (this) {
         buffer.append(a);
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
     }
@@ -322,7 +320,7 @@ public void println(String s) {
       String msg;
       synchronized (this) {
         buffer.append(s);
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
     }
@@ -332,7 +330,7 @@ public void println(Object o) {
       String msg;
       synchronized (this) {
         buffer.append(o);
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
     }
@@ -352,7 +350,7 @@ public PrintStream format(Locale locale, String format, Object... args) {
         if (buffer.indexOf("\n", startLength) < 0) {
           return this;
         }
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
       return this;
@@ -374,17 +372,13 @@ public PrintStream append(CharSequence cs, int start, int limit) {
         if (!flush) {
           return this;
         }
-        msg = flushToString();
+        msg = flushBufferToString();
       }
       publishIfNonEmpty(msg);
       return this;
     }
 
-    // Note to avoid a deadlock, publish may never be called synchronized. See BEAM-9399.
     private void publishIfNonEmpty(String message) {
-      checkState(
-          !Thread.holdsLock(this),
-          "BEAM-9399: publish should not be called with the lock as it may cause deadlock");
       if (message == null || message.isEmpty()) {
         return;
       }
diff --git a/runners/google-cloud-dataflow-java/worker/src/test/java/org/apache/beam/runners/dataflow/worker/logging/JulHandlerPrintStreamAdapterFactoryTest.java b/runners/google-cloud-dataflow-java/worker/src/test/java/org/apache/beam/runners/dataflow/worker/logging/JulHandlerPrintStreamAdapterFactoryTest.java
index ae0396f02e59..eff5f3494791 100644
--- a/runners/google-cloud-dataflow-java/worker/src/test/java/org/apache/beam/runners/dataflow/worker/logging/JulHandlerPrintStreamAdapterFactoryTest.java
+++ b/runners/google-cloud-dataflow-java/worker/src/test/java/org/apache/beam/runners/dataflow/worker/logging/JulHandlerPrintStreamAdapterFactoryTest.java
@@ -133,6 +133,14 @@ public void testLogRawBytes() {
     assertThat(handler.getLogs(), hasLogItem(msg + newlineMsg));
   }
 
+  @Test
+  public void testLogThrowable() {
+    PrintStream printStream = createPrintStreamAdapter();
+    Throwable t = new RuntimeException("Test error");
+    t.printStackTrace(printStream);
+    assertThat(handler.getLogs(), hasLogItem("testLogThrowable"));
+  }
+
   @Test
   public void testNoEmptyMessages() {
     try (PrintStream printStream = createPrintStreamAdapter()) {