The Independent Election Commission (IEC) declared the vote a "major success," but disqualified another three people who won seats according to preliminary results and delayed certified results from one troubled province.
The September 18 parliamentary poll was Afghanistan's second since the 2001 US-led invasion brought down the Taliban, but results took far longer than expected to compile because of investigations into widespread corruption.
The outcome dampened Western hopes that the election would be an improvement on the fraud-tarnished 2009 presidential vote which cast a long pall over President Hamid Karzai's return to power and his pledge to wipe out corruption.
There are no standard political parties in Afghanistan and most of the 2,514 people who stood for 249 seats in the lower house were independent candidates, making it difficult to assess the results' political significance.
Candidates for 238 seats were named, leaving 11 still uncertified due to "technical problems" from the southern province of Ghazni, where Afghanistan's largest ethnic group, the Pashtuns, apparently suffered a crushing defeat.
Preliminary results gave ethnic Hazaras all 11 seats in the province, a flashpoint in the nine-year Taliban insurgency.
IEC chairman Fazil Ahmad Manawi said Ghazni had the largest number of polling stations shut due to insecurity.
"Even in areas where polling sites were open, people did not turn up to vote," Manawi said. In one district, for instance, only three votes were cast.
Likely to spark further controversy, a senior election official speaking on condition of anonymity said Pashtuns, the war-torn country's traditional rulers, won about 88 seats in the new lower house compared to 112 last time.
Election authorities have already invalidated about 1.3 million of the 5.6 million votes cast after receiving more than 5,000 complaints of fraud in the wake of the poll. Of those, 2,500 complaints were classed as "serious".
Manawi said a total of 24 candidates had been stripped of victory accorded to them by preliminary results.
At least three were disqualified because they failed to resign from government jobs. The group is understood to include allies of Karzai and even a first cousin of the president.
Karzai, himself a Pashtun, has favoured a re-run in Ghazni and on Wednesday the presidency stopped short of immediately accepting the poll outcome.
"We haven't seen the results yet," Karzai's spokesman Waheed Omer told AFP when asked whether the president had accepted the results.
An election official told AFP that another vote in Ghazni was unlikely.
"The other option is that elections will be suspended for an unknown time and according to electoral law, the current members of parliament from Ghazni will continue their jobs," said the official, Zakaria Barakzai.
Nader Nadery, chairman of watchdog, the Free and Fair Election Foundation of Afghanistan, said it was too early to assess the new parliament.
"But one thing is very clear -- we have a number of bad faces that are still there. We have a number of new faces elected too," Nadery told AFP.
Afghanistan's previous parliament was dominated by warlords, many of them accused of war crimes.
About 100 failed candidates marched in Kabul on Wednesday, denouncing the results as fraudulent.
Losing candidates have staged a number of protests across the country, accusing electoral officials of taking bribes and victorious rivals of stuffing ballot boxes.
Wednesday's results were announced a day after a Pentagon report admitted that violence in Afghanistan was now at an all-time high as US-led Nato forces try to roll back the Taliban from cities and towns.
Nato leaders last week endorsed a plan to start handing Afghan forces command of the war next year, with the aim of ceding full control by 2014. The United States and Nato currently have around 143,000 troops in Afghanistan.
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