The gunmen, dressed in the uniform of Pakistani security forces, carried out Tuesday's attack in the Mach area of Balochistan province.
Separatists kidnapped 23 labourers and security forces personnel after blocking the road, with 14 of them being killed in the attack.
Mach is in the Bolan district of Balochistan, about 70km from Quetta, the provincial capital.
"Miscreants blocked the road in two places. First they took away five FC [paramilitary] men from an FC patrol vehicle, tied them up and snatched their walkie-talkies and weapons," provincial home secretary Akbar Hussain Durrani told the AFP news agency.
The rebels then stopped four buses and took away the 23 people. Nine of them, including six security forces personnel, were then released, Durrani told Al Jazeera.
When security forces personnel confronted the attackers, the rebels fired off a rocket that killed one security officer, Durrani said.
"Then they lined them up in the mountains and killed 13 [of the people kidnapped]," added Durrani. Local official, Kashif Nabi, confirmed the incident and said the bodies had been recovered.
"We are making arrangements to bring them to Quetta," he said.
Rebel groups in Balochistan say that the Pakistani state deprives those of Baloch origin of their rights, and have been fighting for independence from Pakistan for decades.
In response, the Pakistani military has carried out a brutal crackdown on such groups.
Durrani told Al Jazeera that authorities would be launching a "special operation" in response to Tuesday's raid.
Violence in Balochistan has been particularly intense since the killing of Akbar Bugti, a Baloch separatist leader who was previously part of the government in 2006.