diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/StreamCopyThread.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/StreamCopyThread.java
index eabe72b25..3ee1a2d6f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/io/StreamCopyThread.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/io/StreamCopyThread.java
@@ -61,6 +61,9 @@ public class StreamCopyThread extends Thread {
 
 	private final AtomicInteger flushCount = new AtomicInteger(0);
 
+	/** Lock held by flush to avoid interrupting a write. */
+	private final Object writeLock;
+
 	/**
 	 * Create a thread to copy data from an input stream to an output stream.
 	 *
@@ -75,6 +78,7 @@ public class StreamCopyThread extends Thread {
 		setName(Thread.currentThread().getName() + "-StreamCopy"); //$NON-NLS-1$
 		src = i;
 		dst = o;
+		writeLock = new Object();
 	}
 
 	/**
@@ -86,7 +90,9 @@ public class StreamCopyThread extends Thread {
 	 */
 	public void flush() {
 		flushCount.incrementAndGet();
-		interrupt();
+		synchronized (writeLock) {
+			interrupt();
+		}
 	}
 
 	/**
@@ -118,12 +124,12 @@ public class StreamCopyThread extends Thread {
 			for (;;) {
 				try {
 					if (readInterrupted) {
-						try {
+						synchronized (writeLock) {
+							boolean interruptedAgain = Thread.interrupted();
 							dst.flush();
-						} catch (InterruptedIOException e) {
-							// There was a new flush() call during flush previous bytes
-							// need continue read/write/flush for the new bytes
-							continue;
+							if (interruptedAgain) {
+								interrupt();
+							}
 						}
 						readInterrupted = false;
 						if (!flushCount.compareAndSet(flushCountBeforeRead, 0)) {
@@ -148,20 +154,26 @@ public class StreamCopyThread extends Thread {
 					if (n < 0)
 						break;
 
-					boolean writeInterrupted = false;
-					for (;;) {
-						try {
-							dst.write(buf, 0, n);
-						} catch (InterruptedIOException wakey) {
-							writeInterrupted = true;
+					synchronized (writeLock) {
+						if (isInterrupted()) {
 							continue;
 						}
 
-						// set interrupt status, which will be checked
-						// when we block in src.read
-						if (writeInterrupted || flushCount.get() > 0)
-							interrupt();
-						break;
+						boolean writeInterrupted = false;
+						for (;;) {
+							try {
+								dst.write(buf, 0, n);
+							} catch (InterruptedIOException wakey) {
+								writeInterrupted = true;
+								continue;
+							}
+
+							// set interrupt status, which will be checked
+							// when we block in src.read
+							if (writeInterrupted || flushCount.get() > 0)
+								interrupt();
+							break;
+						}
 					}
 				} catch (IOException e) {
 					break;