MP is under military. civilian police should and must have jurisdiction over military, its just another arm of state. in india IB investigates military (corruption spying anything).
PK can tell about the up to date info.
When a military vehicle gets out of cantt area, it travels under permit. That permit has all the information of the reason why its travelling and permit is stamped by MP. Now lets say the military vehicle is parked somewhere or its stopped. Police approaches it, the driver or the second seater or the officer can show the police that permit. Then Police has to communicate with MP since the military vehicle (with broad arrow) is responsibility of MP for legal and other matters.
Bottom line, MP has to get involved this way or other.
Now the issue in Pakistan is many fold. A staff car (with or without plates open). Ok if you dont know plates open or not, let me explain that first.
Plates Open like below means officer is travelling in the vehicle, in this case its 2-sar so a Major General.
Plates covered or closed, means that officer is not in the vehicle, just driver or driver with family or driver with guard or driver with PA etc, like below
So Police doesn't stop if plates are open, in fact even MP doesn't stop when plates are open, where as MP has the right to stop and check, so can police, but its the culture that its an officer on duty and in uniform so he passes and is saluted at by MP and Police.
Now lets talk of other scenarios.
This below is vehicle on patrol, Police will not stop it.
The below vehicle is going for administration duty or for any other task inside city, so police can stop it, but the driver will show permit to police or display permit on windshield so Police can stop, read permit and let it go
For this one below, the convoys are led and guided by MPs, so police will not become involved.
Then police knows that certain military vehicles will travel on certain routes everyday. Police's own special branch personnel are standing with FIU (Field intel units) of Army. The FIU is undercover intel which keeps an eye on military personnel and military vehicles. They exchange information with police special branch especially when there is a " route " of movement for VIP's or convoys.
For military vehicle movement inside city or on specific routes, MP informs police that such and such military vehicles will be passing or patrolling or an ADM duty so the police keeps the traffic open or already knows that military vehicles will visit that area.
I mentioned culture. This is important, police is weak, sorry to say. Even if they stop a military vehicle or staff car, they know they wont find anything and MP or the officer will inform their superiors as to why military vehicles are being checked when all clearance is given by MP and unit for the vehicle to move.
Police knows it will have to deal with MP at any stage if it stops a military vehicle. The MP unit covers all legalities or they badly face music so the paper work of vehicles is up to date. Unit MT also knows that a problem with paper work will cause delays so they don't want to give excuse to MP.
Other commuters like private vans, cars, buses etc are easy targets for money also, so Police will not waste time on Military vehicles. Even public doesn't listen to police, but I have seen that mostly there is comradeship between uniformed personnel (Police + Army) so military vehicle drivers do cooperate especially when officers are not in vehicle, since police salutes the officers and asks the vehicle to proceed.
In some cases, I have seen that military vehicles stop next to police check points if they are waiting for something, they feel it safer to stop/park vehicle there, get a drink, use the loo or share a ciggie etc.