The negotiations on Monday involve a possible reopening of some polling stations and Qanuni's casting of his own vote after he boycotted the election on Saturday, his aide Hamid Nuri said.
A senior spokesman for the joint UN-Afghan election commission Ultan Muhammad Bahin said it was "discussing a request by Qanuni, and other issues related to weather conditions, either to open ballot boxes or not".
"Discussions are ongoing," he said.
Nuri said if polling stations were reopened, "all those candidates including Qanuni who have not voted will cast their vote".
Part of the agreement would involve the setting up of an investigation into the irregularities in the election, Nuri added.
Qanuni was among 14 presidential candidates who on Saturday called for a halt to the election, charging fraud and irregularities.
Northern Alliance support
Most of the candidates stood no chance of winning, apart from Qanuni, who has the support of powerful Northern Alliance figures who held key posts in Karzai's cabinet.
Election officials were already preparing to investigate complaints about the vote, despite Taliban threats of violence and calls to boycott the vote.
First election results could be
available later this week
The United Nations said counting of ballots was not due to start until "two to four days" after Saturday's vote, and the first results could be available later this week, with final results another two to three weeks away.
"I've always said that the actual counting of the ballots would not start before two to four days," UN spokesman Manoel de Almeida e Silva said.
"I think it would be fair to imagine in three, four days the first results of the counting" would be available, he added, although "the estimate is that final results will take two to three weeks".
Ballot boxes were being transported to eight counting centres by air and road, "using trucks, helicopters, airplanes and even the now famous donkeys and horses", he said on Sunday.
If, as expected, US-backed Karzai wins, the focus will shift to whether he has a legitimate mandate to rule the fractious country despite the objections of his opponents.
The opposition candidates include powerful regional and ethnic leaders - some of whom have large private militias - and UN and Western diplomats are working hard to ensure they accept the result.
A run-off election will be held if the winner does not secure more than 50% of the vote.
Afghanistan has been shattered by 25 years of conflict, including foreign invasions and civil war.
Karzai told a news conference on Sunday there would be "no horse trading" if he won the election, but it is widely expected that Qanuni would be offered a senior position if he accepts the outcome.
Some of the other protesting candidates have already softened their initial call for the election to be scrapped and held again, saying they would accept the findings of an independent inquiry.