The defence ministry said they were not troops. Kandahar provincial police chief Mutihullah Khan Qatah said there were 50 passengers aboard the bus when it was ambushed Thursday in Maiwand district about 50 kilometres (30 miles) east of Kandahar city.
"Among them 10 people were released after they were said to be civilians. The rest of them were killed," he told AFP.
Six bodies were in the district clinic and about two dozen more were believed to be in a Taliban-controlled area, Qatah told a media briefing later. "We are still trying to find them." The police chief said the men, all apparently aged between 20 and 25 and in civilian clothes, were from Kabul and travelling to Iran to seek work in the neighbouring country. Hundreds of Afghans work illegally in Iran.
After they were captured they had been divided into two groups of about 20 and taken to different areas, he said.
Another bus had been able to escape, although the Taliban opened fire on it and killed a child and wounded a man, he said. Defence ministry spokesman General Mohammad Zahir Azimi said his reports were that the six bodies recovered Sunday were all beheaded. Another 25 were believed to be in the neighbouring province of Helmand, he said.
A Taliban spokesman, Yousuf Ahmadi, claimed the captured bus was taking Afghan National Army reinforcements to volatile Helmand. "We found government documents on them and we killed 27 of them. The rest, who were civilians, we freed," he said. The bodies had been dropped in groups of two to four around the area, he said.
Neither the government or insurgent tolls could be independently confirmed. Helmand has seen intense fighting in recent weeks, with a series of attacks on the provincial capital Lashkar Gah last week. The government and international troops, mainly British, control some centres but admit that several districts are held by the insurgents.
But Helmand government spokesman Daud Ahmadi said the military never used local civilian transport. "These people who have been killed are all those people who were going from Kabul to Iran for work," he said.
Maiwand, where the bus was ambushed, is in an area where the Taliban took up arms in the early 1990s to sweep into government by 1996. The extremists were removed in 2001 in a US-led invasion. They are waging an insurgency to take back power in a campaign that targets soldiers and government officials.
About 150 labourers were kidnapped in the western province of Farah late last month, also while travelling by bus. Their kidnappers had also claimed to be part of the Taliban, although this was rejected by the militia's spokesmen.
The group were carpenters, masons and other labourers employed by a US construction company and working on a project for the Afghan National Army. Authorities said they were all freed after around a week. The insurgency, which surged in 2005, has killed at least 4,000 people in Afghanistan this year and the growing violence has alarmed the country and its international partners.