Three of them belong to Karachi, one to Gilgit and one to Rawalpindi, police said.
"The bodies bear torture marks and bullet wounds. It appears that the five men were first tortured and then shot dead," a police official said.
The bodies were found near Noori Jam Tamashi shrine at Kinjhar lake in Thatta, some 100 km from Karachi.
"We are still trying to find out the motive behind these killings but all five men have been identified," the official said.