diff --git a/cmd/runmqserver/qmgr.go b/cmd/runmqserver/qmgr.go
index 49b73c1..821bd66 100644
--- a/cmd/runmqserver/qmgr.go
+++ b/cmd/runmqserver/qmgr.go
@@ -16,7 +16,7 @@ limitations under the License.
 package main
 
 import (
-	"io"
+	"bytes"
 	"io/ioutil"
 	"os"
 	"os/exec"
@@ -86,43 +86,35 @@ func configureQueueManager() error {
 		log.Println(err)
 		return err
 	}
-
 	for _, file := range files {
 		if strings.HasSuffix(file.Name(), ".mqsc") {
 			abs := filepath.Join(configDir, file.Name())
 			// #nosec G204
 			cmd := exec.Command("runmqsc")
-			stdin, err := cmd.StdinPipe()
+			// Read mqsc file into variable
+			mqsc, err := ioutil.ReadFile(abs)
 			if err != nil {
-				log.Println(err)
-				return err
+				log.Printf("Error reading file %v: %v", abs, err)
+				continue
 			}
-			// Open the MQSC file for reading
-			// #nosec G304
-			f, err := os.Open(abs)
+			// Write mqsc to buffer
+			var buffer bytes.Buffer
+			_, err = buffer.Write(mqsc)
 			if err != nil {
-				log.Printf("Error opening %v: %v", abs, err)
+				log.Printf("Error writing MQSC file %v to buffer: %v", abs, err)
+				continue
 			}
-			// Copy the contents to stdin of the runmqsc process
-			_, err = io.Copy(stdin, f)
-			if err != nil {
-				log.Errorf("Error reading %v: %v", abs, err)
-			}
-			err = f.Close()
-			if err != nil {
-				log.Errorf("Failed to close MQSC file handle: %v", err)
-			}
-			err = stdin.Close()
-			if err != nil {
-				log.Errorf("Failed to close MQSC stdin: %v", err)
-			}
-			// Run the command and wait for completion
+			// Buffer mqsc to stdin of runmqsc
+			cmd.Stdin = &buffer
+			// Run runmqsc command
 			out, err := cmd.CombinedOutput()
 			if err != nil {
 				log.Errorf("Error running MQSC file %v (%v):\n\t%v", file.Name(), err, strings.Replace(string(out), "\n", "\n\t", -1))
+				continue
+			} else {
+				// Print the runmqsc output, adding tab characters to make it more readable as part of the log
+				log.Printf("Output for \"runmqsc\" with %v:\n\t%v", abs, strings.Replace(string(out), "\n", "\n\t", -1))
 			}
-			// Print the runmqsc output, adding tab characters to make it more readable as part of the log
-			log.Printf("Output for \"runmqsc\" with %v:\n\t%v", abs, strings.Replace(string(out), "\n", "\n\t", -1))
 		}
 	}
 	return nil
diff --git a/test/docker/docker_api_test.go b/test/docker/docker_api_test.go
index 37759f2..f540639 100644
--- a/test/docker/docker_api_test.go
+++ b/test/docker/docker_api_test.go
@@ -554,6 +554,49 @@ func TestMQSC(t *testing.T) {
 	}
 }
 
+// TestLargeMQSC creates a new image with a large MQSC file in, starts a container based
+// on that image, and checks that the MQSC has been applied correctly.
+func TestLargeMQSC(t *testing.T) {
+	t.Parallel()
+	cli, err := client.NewEnvClient()
+	if err != nil {
+		t.Fatal(err)
+	}
+	const numQueues = 1000
+	var buf bytes.Buffer
+	for i := 1; i <= numQueues; i++ {
+		fmt.Fprintf(&buf, "* Test processing of a large MQSC file, defining queue test%v\nDEFINE QLOCAL(test%v)\n", i, i)
+	}
+	var files = []struct {
+		Name, Body string
+	}{
+		{"Dockerfile", fmt.Sprintf(`
+          FROM %v
+          USER root
+          RUN rm -f /etc/mqm/*.mqsc
+          ADD test.mqsc /etc/mqm/
+          RUN chmod 0660 /etc/mqm/test.mqsc
+          USER mqm`, imageName())},
+		{"test.mqsc", buf.String()},
+	}
+	tag := createImage(t, cli, files)
+	defer deleteImage(t, cli, tag)
+
+	containerConfig := container.Config{
+		Env:   []string{"LICENSE=accept", "MQ_QMGR_NAME=qm1"},
+		Image: tag,
+	}
+	id := runContainer(t, cli, &containerConfig)
+	defer cleanContainer(t, cli, id)
+	waitForReady(t, cli, id)
+
+	rc, mqscOutput := execContainer(t, cli, id, "mqm", []string{"bash", "-c", "echo 'DISPLAY QLOCAL(test" + strconv.Itoa(numQueues) + ")' | runmqsc"})
+	if rc != 0 {
+		r := regexp.MustCompile("AMQ[0-9][0-9][0-9][0-9]E")
+		t.Fatalf("Expected runmqsc to exit with rc=0, got %v with error %v", rc, r.FindString(mqscOutput))
+	}
+}
+
 // TestInvalidMQSC creates a new image with an MQSC file containing invalid MQSC,
 // tries to start a container based on that image, and checks that container terminates
 // func TestInvalidMQSC(t *testing.T) {