Election commission Chairman Fazel Ahmad Manawi said recounts have been ordered in parts of at least seven provinces.
He said the number of places subject to recounts was expected to increase because not all results have been fully examined. He said the votes under question would be recounted under the supervision of his commission and the electoral complaints commission, along with national and international observers.
"We want to be very clear on the counting of these ballots," he said.
The Sept. 18 elections were seen as a test of the Afghan government's commitment to rooting out corruption.
The vote was the first since a presidential election last year that was nearly derailed by widespread ballot-box stuffing and tally manipulation. That poll led many Western powers to question whether they should be supporting the administration of President Hamid Karzai with military forces and funds.
About 2,500 candidates are vying for 249 parliamentary seats. Final results are not expected until late next month.
Election day was marred by rocket attacks and bombings at polling stations. At least 21 civilians and nine police officers were killed during the voting, according to the election commission and the Interior Ministry.
Observers said some people were able to wash off supposedly indelible ink used to mark fingers to prevent multiple voting. In some areas, poll workers let people use fake registration cards and allowed children to vote, according to the Free and Fair Election Foundation of Afghanistan, the main independent Afghan observer group.
NATO spokesman Rear Admiral Greg Smith said violence this time was higher than in the previous poll, with 396 incidents compared to 281 before. He said part of the reason for the increased number of reported incidents was that NATO forces are more numerous in the country now and are in a better position to monitor the situation.
Also Sunday, Britain's Foreign Office said it is urgently investigating the disappearance of a U.K. citizen in Afghanistan, but declined to provide further details or specify the region where the person had disappeared.
In a statement from London, the Foreign Office said it was "working with other international partners to urgently investigate these reports."
In the south, two NATO service members were killed in a bomb blast, the military alliance said.
NATO said the troops were killed by a homemade bomb, but provided no further details. The nationalities of NATO deaths are not generally released until after the next of kin have been contacted.
This year is already the deadliest of the war, with more than 530 international forces killed. There are about 140,000 foreign troops in Afghanistan, including about 30,000 additional troops brought in under President Barack Obama's surge strategy.
NATO said Sunday that an air strike following a cross-border attack on an Afghan National Security Force outpost in Khost province, near Pakistan, on Friday killed more than 30 insurgents. A follow up on Saturday resulted in several more insurgents killed. It said there were no NATO casualties.
The coalition also said it killed at least five insurgents during a clearing operation in Kandahar, the Taliban heartland in the south that remains particularly volatile.
The multi-day operation was intended to impede the Taliban's ability to move freely in the area and to disrupt its attempts to stage attacks. According to a NATO statement Sunday, the militants fought back with rocket-propelled grenades, machine-gun and small-arms fire. It said no Afghan or coalition troops were killed.
NATO said Sunday that two Afghan civilians riding a motorcycle were killed Saturday after failing to stop while approaching a security perimeter in Helmand province in the south.
It said the motorcycle driver briefly stopped but then ignored warnings and accelerated toward the security forces.
By Associated Press Writer Eric Talmadge. Rahim Faiez contributed to this report