Is it correct to compare two values resulting from a call to System.nanoTime() on two different machines? I would say no because System.nanoTime() returns a nanosecond-precise time relative to some arbitrary point time by using the Time Stamp Counter (TSC) which is processor dependent.
If I am right, is there a way (in Java) to capture an instant on two different machines and to compare (safely) these values with at least a microsecond precision or even nanotime precision?
System.currentTimeMillis() is not a solution because it is not returning a linearly increasing number of time stamps. The user or services such as NTP can change the system clock at any time and the time will leap back and forward.
You might want to look into the various clock synchronization algorithms available. Apparently the Precision Time Protocol can get you within sub-microsecond accuracy on a LAN.
If you don’t need a specific time value but rather would like to know the ordering of various events, you could for instance use Lamport timestamps.