You want the system time via JNI or JNA. This can have micro second resolution.
What I do is use nanoTime for short intervals with a currentTimeMillis at the start of an event for context. Ie i dont try to solve this problem in real time.
Note: currentTimeMillis is not monotonically increasing and can go backwards.
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We're using gettimeofday over JNR. It's much faster than JNA; 250 ns per call on average.