Congratulations, you found one of java's oldest shortcomings.
System.currentTimeMillis() is the only way to measure time without any additional packages/libraries.
If you want to use an additional library:
LWJGL, Java3D and GAGE all have a high resolution timer.
Use LWJGL if you are planning to go for max performance 3D graphics and sound using openGL/openAL, use java3D of you want a convenient general purpose 3D scenegraph API or GAGE if you want to create games using the standard java API's.
(The authors will surely correct me if I'm wrong somewhere