Polls were due to close at 4:00 p.m. local time but as that hour approached, thousands of people around the country remained in lines at polling stations waiting to cast their ballots.
Rivals to Afghan Transitional Administration Chairman Hamid Karzai have complained of irregularities and violations and called for the vote to be halted.
The Joint Election Management Body (JEMB) rejected that call, but JEMB Vice Chairman Ray Kennedy did say claims made by Karzai's opponents will be investigated.
"The JEMB wishes to reassure voters, candidates, and observers that procedures exist to receive, investigate and decide on complaints," Kennedy said. "All complaints and irregularities raised with the JEMB will be thoroughly investigated and will be taken into account when the JEMB deliberates on the extent to which the election accurately reflects the will of the Afghan people."
Among the complaints are that the ink used to mark voters' fingers to prevent them from casting more than one ballot washed away easily, and that supporters of some candidates continued campaigning outside voting centers despite prohibitions.
[For more on the Afghan elections, see RFE/RL and Radio Free Afghanistan's dedicated "Afghanistan Votes 2004-05"