The remarks were the clearest indication yet that the election board will acknowledge irregularities during the Oct. 9 election - the key condition set by Karzai's closest rival for conceding defeat.
"Some boxes were so obviously stuffed that we don't believe they were legitimately cast votes," Ray Kennedy, the deputy chairman of the joint U.N.-Afghan electoral commission, told The Associated Press.
With almost all of the approximately 8.2 million votes cast in the Oct. 9 election already counted, the U.S.-backed incumbent has secured an unassailable lead and the majority needed to avoid a run-off.
But the electoral board insists it will wait for the results of investigations into fraud allegations brought by Karzai's rivals before calling the result.
Officials say that could take until the weekend.
Karzai has been the interim leader since the fall of the Taliban in late 2001. An election victory would make him Afghanistan's first popularly chosen leader after a quarter century of war and give him a five-year term, in which he has pledged to raise the country's standard of living.
It could also provide a foreign policy boost to Afghanistan's main sponsor, President Bush, in his own bid for re-election next week.
On Tuesday, election managers toured Afghanistan, examining some 400 ballot boxes quarantined at counting centers because of allegations of fraud, problems with paperwork and damaged seals.
Kennedy led a team to the northern city of Kunduz. Other teams were bound for Gardez, in the southeast, and Kandahar, Afghanistan's main southern city.
Kennedy said there would "almost inevitably be some (ballot) boxes excluded from the count" because of irregularities, but agreed that even if every quarantined ballot was thrown out, it wouldn't be enough to push Karzai below the 50-percent mark.
"That's my sense at this point," he said.
With 97.7 percent of ballots counted, Karzai has 55.4 percent of the votes, 39 points ahead of his closest rival, former Education Minister Yunus Qanooni.
Qanooni and the third-placed candidate, former Planning Minister Mohammed Mohaqeq, have refused to concede defeat, claiming that Karzai was ahead thanks to massive fraud.
Still, Qanooni has said he is willing to accept the result to avoid fanning tensions in the country - provided the irregularities are publicly acknowledged.
While irregularities detected during the counting process are under examination by the electoral board's legal experts, a panel of foreign election specialists is looking separately into problems on polling day.
The three-member panel was established after Qanooni and 14 other candidates threatened to boycott the poll because of a mix-up with ink used to mark people's fingers to prevent multiple voting.
On Monday, representatives of several candidates met with the panel at the main United Nations compound in central Kabul. Panel members said they were still days away from completing their report.
The panel must report to the electoral board before officials can decide whether to declare the election "free and fair."
By Stephen Graham and Matthew Pennington