You may want to look at: https://www.opensc-project.org/opensc/wiki/Java
Smart card access itself can be handled natively:
An example from the java doc (edited for readability):
// show the list of available terminals
TerminalFactory factory = TerminalFactory.getDefault();
List<CardTerminal> terminals = factory.terminals().list();
System.out.println("Terminals: " + terminals);
// get the first terminal
CardTerminal terminal = terminals.get(0);
// establish a connection with the card
Card card = terminal.connect("T=0");
System.out.println("card: " + card);
CardChannel channel = card.getBasicChannel();
ResponseAPDU r = channel.transmit(new CommandAPDU(c1));
System.out.println("response: " + toString(r.getBytes()));
// disconnect
card.disconnect(false);