Aren't the whatsapp messages sent over the net? I.e. wouldn't it be the case that the government could only see the outgoing IP address? I guess if they were very well organized and working with the telecoms, they could then maybe see the outgoing IP and assuming that IP were on a telecom network they also controlled they could turn that into a person. This is all assuming that they could even figure out which encrypted outgoing packets correspond to calls (maybe this isn't too bad considering call streams would maybe have a fairly standard packet rate, etc.?).

Either way seems pretty hard without direct help from whatsapp.