I can't help but think someone is pulling your leg. The Java compiler converts Java source to byte code. In the old days, programmers occasionally wrote critical parts of their application in machine language for performance reasons, which I guess is the moral equivalent of byte code. Those days are fortunately over.
If you really need the additional performance you should make sure to do a JIT or Hotspot compile. Your only other option is to write it in C as a native method and do the JNI integration.
Yes you could write your application using bytecode. I can think of only one assembly tool that did so but it has not been updated for a few years and may be out of date. The name of the tool is Jasmin and can be found at the following at http://mrl.nyu.edu/~meyer/jvm/. However, this will require you to write an entire class or set of classes using bytecode, it does not allow you to mix Java and bytecode together.
The only other alternative is to gain an understanding about the Java class file format so that you could modify the bytecode of critical methods for optimum performance. Check out the Java Virtual Machine Specification for more information.
There are also several tools designed to create class files (without a compiler), modify existing class files, and read class files. One of the better tools is called the Bytecode Engineering Library and can be found at http://bcel.sourceforge.net/. You could use this, along with a good understanding of bytecode, to modify the bytecode of any class.