The killings on Friday night in the province of Zabul were the most serious attack yet on the elections, which the Taliban and allied fighters have vowed to disrupt.
News of the violence came a day after a bomb killed two women working for the UN-Afghan electoral body and wounded nine women poll workers and two children in the eastern city of Jalalabad.
Haji Ubaid Allah, chief of Khas Uruzgan district in the central province of Uruzgan, said the fighters stopped a bus carrying 17 civilians through the district on Friday.
They took the passengers to Dai Chopan district of the neighbouring province of Zabul and killed all but one when they found they were carrying voter registration cards, he quoted the lone survivor as saying.
"They were apparently killed because they were carrying the registration cards," he said.
A spokesman for the United Nations, which is overseeing voter registration, said he had no information about the incident.
Uruzgan police chief Roozi Khan said several hundred US and Afghan soldiers backed by air support were searching for the villagers' bodies and the attackers.
"We have been told that the group involved in this incident has hidden in Deh Rawud district of Uruzgan," he said.
A Taliban spokesman claimed responsibility for killing the women in Jalalabad on Saturday by bombing their bus. He said the movement had warned Afghans not to become involved in elections that would only strengthen the US-backed government.
Taliban spokesman Abd al-Latif Hakimi said the Taliban had killed 19 people kidnapped in Uruzgan on Friday but none of them were civilians.
Afghan soldiers searched for
"Six of them belonged to the elections commission and 13 were government soldiers," he said when contacted by satellite telephone.
An upsurge in violence in the run-up to the polls has raised doubts as to whether they can be held on time.
About 4.5 million of nearly 10 million voters eligible have registered, but the process has been slowed in the south and east by threats and violence. Female registration has lagged, partly because of problems recruiting female election workers.
The latest attacks are further setbacks for President Hamid Karzai's efforts to bring peace to Afghanistan, a country US President George Bush has described as a role model for Iraq.
Karzai appealed to NATO on Friday to make good its pledge to send more troops to protect the presidential and parliamentary polls to ensure they can be held as scheduled.
At a summit in Istanbul starting on Monday, NATO is to announce that its 6400-strong peacekeeping force will take command of more military-civilian reconstruction teams in northern Afghanistan and deploy about 1200 troops for the polls.
But this will fall short of the figure of at least 5000 extra troops the government and the United Nations say are needed, and the deployments will be to relatively secure areas, not to the south and east where militants are most active.
Analysts say Bush, Karzai's main supporter, wants a September poll so that he has a foreign policy success to balance against Iraq before his own re-election bid in November.