AS/400 は使ったこと無いですが､ﾈｯﾄで調べてみた限りでは､

CommandCall ｸﾗｽ(IBM Toolbox for Java のｸﾗｽ)の run() ﾒｿｯﾄﾞで呼べそうです｡

■ IBM Toolbox for Java

http://publib.boulder.ibm.com/infocenter/iseries/v5r4/topic/rzahh/page1.htm

■ ｺﾏﾝﾄﾞ呼び出し

http://publib.boulder.ibm.com/infocenter/iseries/v5r4/topic/rzahh/cmdc.htm

■ CommandCall - com.ibm.as400.access.CommandCall

http://publib.boulder.ibm.com/infocenter/iseries/v5r4/topic/rzahh/javadoc/com/ibm/as400/access/CommandCall.html

import java.io.*;
import java.util.*;
import com.ibm.as400.access.*;

public class CommandCallExample extends Object
{
 public static void main(String[] parmeters)
 {
 AS400 sys = new AS400("mySystem.myCompany.com");
 CommandCall cmd = new CommandCall(sys);
 try
 {
 cmd.run("CRTLIB MYLIB");
 AS400Message[] messageList = cmd.getMessageList();
 }
 catch (Exception e)
 {
 System.out.println("Command " + cmd.getCommand() + " issued an exception!");
 e.printStackTrace();
 }
 }
}