The attackers are reported to have checked the identity cards of all the passengers before removing the Shias and shooting them.
About 27 other passengers on the bus were spared.
Meanwhile, a Chinese woman was shot dead with a Pakistani male companion in the city of Peshawar, police say.
Bus attack
Kohistan is not known for militancy, but it borders the Swat valley, which has had a Taliban presence in the past.
The attack took place close to the remote and mountainous area of Harban Nala, approximately 130 miles (208 km) north of the capital, Islamabad.
Four buses were travelling in a convoy from the city of Rawalpindi to the northern town of Gilgit.
“Armed men hiding on both sides of the road attacked,” local police chief Mohammad Ilyas told the Agence France-Presse news agency. Local officials say that the men who ambushed the bus were wearing military fatigues.
It happened in an area dominated by Sunni tribes, Reuters quotes a policeman as saying.
Prime Minister Yousuf Raza Gilani has condemned the attack, insisting that such incidents would not deter the government in its resolve to fight “the menace of terror”.
Correspondents say that more than two-thirds of Kohistan’s 500,000 people live a nomadic life and move up and down the country in search of pastures.
Kohistan is 7,400 sq km of sheer mountains, rising from 2,400m (7,874 ft) to 3,700m (12,139 ft) with virtually no plains.
Sunni extremists allied to or inspired by al-Qaeda and the Taliban routinely attack government and security targets in north-west Pakistan, in addition to religious minorities and other Muslim sects they consider to be infidels.
The BBC’s Aleem Maqbool in Islamabad reports that there are frequently complaints from Shias that the Pakistani state does little to stop the attacks and has even released from custody notorious militants accused of carrying them out.
Last month more than 30 Shias were killed in an attack on a mosque in north-west Pakistan.
Chinese targets
The Chinese woman, 40, and her Pakistani companion, 22, were killed by gunmen on motorbikes while walking in the Kohati bazaar area in the historic centre of Peshawar, police said.
It was the fifth shooting or bomb attack in north-western Khyber Pakhtunkhwa province since Thursday, raising concerns that violence is worsening following a relative lull in recent months.
The father of the dead Pakistani said that his son had been working as a translator for the Chinese woman while he was on holiday from studying English literature at university.
The BBC’s M Ilyas Khan in Islamabad says that while a motive for the attack is unclear, it is not unusual for Chinese people to be targeted in Pakistan.
- In 2009 a Chinese engineer was kidnapped in the Dir region of north-west Pakistan. He was released after five months
- A Chinese beautician kidnapped during the Red Mosque siege of 2007 was released several months after being abducted
- One of two Chinese engineers kidnapped by militants loyal to Taliban commander Abdullah Mehsud in 2004 was killed during a rescue bid by Pakistani forces.