Are there protocols for naval vessels in communicating with ships of other governments?

Answer 1

Unless the vessels are military allies (e.g., NATO), where communication is typically over established channels and with established protocols, communication is typically done in accordance with international Maritime Standards and Law. There are specific radio frequencies, flag signals and other methods for signaling vessels of any flag, and ship Captains are expected to know. This also applies to Allied vessels even if they're using specific communication - Captains are expected to obey International Law first unless it's a battle situation.

For those who don't know or feign ignorance, a shot across the vessel's bow is a universally recognized signal to heave to if the vessel doesn't respond and is entering a restricted area.

For navigation near port and in open ocean, there are international maritime "Rules of the Road", instructing how ships are to maneuver when approaching each other, how to navigate in certain waters, etc. Maritime regulations, though they have evolved, are based on ancient maritime customs that haven't changed much, though they've been modernized for current times. All ships typically have military and civilian communication equipment aboard.