I used the following procedure to configure my Windows 2012 server to use NTP running on my linux server.

Configure the Window Time service to use the NTP server:

PS > w32tm /config /manualpeerlist:NameOrIPAddress /syncfromflags:MANUAL

Example:

PS > w32tm /config /manualpeerlist:192.168.0.1 /syncfromflags:MANUAL

Stop the Windows Time service:

PS > Stop-Service W32Time

Start the Windows Time service:

PS > Start-Service W32Time

Query the Windows Time service:

PS > w32tm /query /status