Yes; the setProperty() method in the java.lang.System class can set these. Be careful because some properties take effect during JVM startup, and using setProperty() for these will not have the intended effect.
I think you can use policytool that comes with the jre(?)/jdk install to give your program permissions. The permissions would have to be set on every computer that you run your program on. You'll have to read a tutorial to understand how to use policytool. In some cases I've have to manually edit the .java.policy file to get the correct paths to give my programs permissions. There has been a lot of try this, try that until I've been able to give my programs permissions. Perhaps you won't have to do this.