What is a Secrecy Order in patent law?

A Secrecy Order is an official directive issued by the Commissioner for Patents when notified by the chief officer of a defense agency that publication or disclosure of an invention through a patent grant would be detrimental to national security. As stated in 37 CFR 5.2(a):

When notified by the chief officer of a defense agency that publication or disclosure of the invention by the granting of a patent would be detrimental to the national security, an order that the invention be kept secret will be issued by the Commissioner for Patents.

This order restricts disclosure of the invention and delays the grant of a patent until the order is rescinded.