At first I want to let you know that this question is not related with What is native implementation in Java. I got many useful information from that thread.
I want
Yes, see os::javaTimeMillis in /src/os/solaris/vm/os_solaris.cpp to see the Solaris implementation for instance.
/src/os/solaris/vm/os_solaris.cpp
There are a few layers of wrappers to get there though, see JVM_CurrentTimeMillis in /src/share/vm/prims/jvm.cpp
/src/share/vm/prims/jvm.cpp