The Electoral Complaints Commission (ECC) said 1,388 complaints had been received specifically about election day irregularities -- which could impact the results -- ahead of a 4 pm (1130 GMT deadline) deadline for submissions.
There are concerns that the ECC could be hard-pressed to handle the volume of complaints, which are expected to rise as preliminary results are posted on its website.
More than 2,500 candidates stood for the 249 seats up for grabs in parliament's lower hose, or Wolesi Jirga, and many of the losers are expected to lodge complaints.
ECC commissioner and spokesman Ahmad Zia Rafaat told AFP that on top of the 1,388 complaints about polling day irregularities, another 1,700 had been lodged relating to problems ahead of the vote.
ECC officials in the southern provinces of Kandahar, Helmand, Uruzgan and Zabul, where the Taliban insurgency has been at its most fierce, said most complaints received related to allegations of multiple voting.
Election officials said more than four million Afghans voted on Saturday in their second parliamentary poll since the 2001 US-led invasion overthrew the Taliban regime, held despite insurgent threats and attacks.
Counting has been completed in most of the country's 34 provinces and first preliminary results are expected on Wednesday.
Final results, due on October 31, can only be announced once complaints have been dealt with and the count certified by the Independent Election Commission (IEC) at its headquarters in Kabul.
Afghan analyst Haroon Mir, who stood for a seat in Kabul, said he would be lodging many complaints, particularly over "problematic" counting and the listing of results.
But he said he feared the ECC would be overwhelmed.
"I'll be doing some complaints. I'm sure there will be plenty of complaints, and the ECC will not have time to review all of them," he said.
Afghanistan's main election observer body, the Free and Fair Election Foundation (FEFA), detailed thousands of election day irregularities, including use of fake voter cards and of underage voting.
FEFA, which fielded almost 7,000 observers across the country, said some were prevented from carrying out their duties.
Some polling centres opened late, and there were widespread allegations of bias by election workers, as well as problems with indelible ink -- supposed to guard against a person voting more than once -- that could be washed off.
The IEC acknowledged in a statement that some fraud was "inevitable" and said it was "fully committed to working with the ECC to eliminate the effect from the final results insofar as possible".
The United Nations' mission in Afghanistan said the electoral institutions were at a "critical stage of fulfilling their duties".
"The independence of these institutions is crucial to the credibility of the completion of the electoral process," it said in a statement.
More than a million ballots were found to be fraudulent in the November poll that returned Hamid Karzai for a second five-year term.
The IEC said early figures from Saturday showed turnout at 40 percent, though analysts said the figure was based on the number of people who would have been eligible to vote in areas where polling centres opened.
More than 1,000 polling centres were not able to open because security could not be guaranteed, and the IEC is expected to say that even more remained closed.
NATO said at least 22 people were killed in polling day violence, with a total of 294 insurgent attacks.
A Pentagon spokesman said election violence was down by a third on the 2009 presidential election.
The United States and NATO's International Security Assistance Force (ISAF) have almost 150,000 troops in the country fighting to bring an end to the war, which is dragging towards its 10th year.
Kabul: Afghanistan's electoral watchdog said on Tuesday it has received over 3,000 complaints about irregularities in the run-up to Saturday's parliamentary election and on polling day itself.
First Published: Tuesday, September 21, 2010, 17:47