All five had been shot in the head, their hands tied behind their backs. The bodies have been taken to a mortuary for further investigation.
Police said the men were residents of Hub, Baluchistan.
"The families have identified them and they claim that they were missing for one and half years," senior police officer Sheeraz Nazir told AFP.
A separatist insurgency has raged in Baluchistan for years and so-called "kill and dump" incidents are common.
No marks of torture were found on the bodies, which the city police chief said had been moved after death.
Hundreds of soldiers and militants have been killed in fighting since the insurgency was revived in 2004.
Suspected Baluch separatist insurgents last month killed at least nine labourers at a poultry farm at Hub.
Rights groups allege security forces have fuelled bloodshed by picking up non-militant separatists, including academics and students, torturing them and dumping their bodies on the streets.
The current insurgency gained in intensity after the 2006 killing of 79-year-old Baluch leader Nawab Akbar Khan Bugti, a revered figure for many rebels.
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