The Arduino development environment is written in Java.
But the standard language you write a program for the Arduino platform is effectively C++.
The Arduino platform is based on an Atmel AVR chip. There is at least one Java VM for AVR chips. There are other languages available for the AVR such as Forth and BASIC (although I could only find commercial versions, so I'll if you want to find them, search for "AVR BASIC").
The Arduino uses a virtual COM port to communicate between the host computer and it. A virtual COM port emulates an old style serial line but is done with USB. You can use the Java communication API to then have a Java program running on the host computer communicate with your physical device.