Why is System.nanoTime() way slower (in performance) than System.currentTimeMillis()?

From this Oracle blog:

System.currentTimeMillis() is implemented using the GetSystemTimeAsFileTime method, which essentially just reads the low resolution time-of-day value that Windows maintains. Reading this global variable is naturally very quick - around 6 cycles according to reported information.

System.nanoTime() is implemented using the QueryPerformanceCounter/ QueryPerformanceFrequency API (if available, else it returns currentTimeMillis*10^6). QueryPerformanceCounter(QPC) is implemented in different ways depending on the hardware it's running on. Typically it will use either the programmable-interval-timer (PIT), or the ACPI power management timer (PMT), or the CPU-level timestamp-counter (TSC). Accessing the PIT/PMT requires execution of slow I/O port instructions and as a result the execution time for QPC is in the order of microseconds. In contrast reading the TSC is on the order of 100 clock cycles (to read the TSC from the chip and convert it to a time value based on the operating frequency).

Perhaps this answer the question. The two methods use different number of clock cycles, thus resulting in slow speed of the later one.

Further in that blog in the conclusion section:

If you are interested in measuring/calculating elapsed time, then always use System.nanoTime(). On most systems it will give a resolution on the order of microseconds. Be aware though, this call can also take microseconds to execute on some platforms.

Most OS's (you didn't mention which one you are using) have an in memory counter/clock which provides millisecond accuracy (or close to that). For nanosecond accuracy most have to read a hardware counter. Communicating with hardware is slower then reading some value already in memory.

It may only be the case on Windows. See this answer to a similar question.

Basically, System.currentTimeMillis() just reads a global variable maintained by Windows (which is why it has low granularity), whereas System.nanoTime() actually has to do IO operations.