"We have evidence the results we have received have been doctored," said Mr Odinga's running mate Kalonzo Musyoka.
He said the vote count should be stopped but added that his comments were not a call for protest.
Counting has been severely delayed after the electronic system crashed.
Following the latest allegation, the Independent Electoral and Boundaries Commission (IEBC) is holding a closed-door meeting with various high commissioners and ambassadors, reports Idris Situma from BBC Swahili.
The chairman of the IEBC is due to address journalists later on Thursday.
Meanwhile the electoral commission's vice-chair, Liliane Mahiri Zaja, told the BBC that no written complaint had so far been received about the way the votes were being counted.
More than 1,000 people were killed in the violence which broke out in 2007-08 after Mr Odinga claimed he had been cheated of victory by supporters of President Mwai Kibaki, who is stepping down after two terms in office.
Mr Kenyatta, who backed Mr Kibaki, is due to stand trial at the International Criminal Court (ICC) next month, accused of organising attacks on members of ethnic groups seen as supporters of Mr Odinga. He denies the charges.
Fall in rejected ballots
Mr Musyoka said the failure of the electronic vote transmission system earlier this week had allowed results to be rigged.
"We as a coalition take the position the national vote-tallying process lacks integrity and has to be stopped and re-started using primary documents from the polling stations," he said on Thursday.
But Mr Musyoka also called on Kenyans to remain calm.
"It is not a call to mass action. We are committed as a coalition to the principle of the rule of law."
Meanwhile, senior members of Mr Odinga's coalition have given the BBC further details about their allegations, saying that the number of ballots counted exceeded that of votes cast at some polling stations.
The long delays, and these new accusations are increasing the tension surrounding the polls, the BBC's James Copnall reports from the capital, Nairobi.
However, until they see comprehensive evidence, many Kenyans will remain sceptical, our correspondent says.
Kenyatta in the lead
Following glitches with hi-tech voting and counting systems, the vote-tallying process was started again from scratch, and by hand, on Wednesday.
Results were only being announced after the ballots had been physically delivered to election headquarters in Nairobi, rather than being filed electronically.
Latest figures show Mr Kenyatta has maintained his lead over Mr Odinga, with 2.7m votes to 2m at 13:00GMT (16:00 Nairobi time) on Thursday. This is in line with the original count.
However, the new tally shows that the number of rejected ballots, which have become a major bone of contention, has fallen sharply.
In the initial count, some 300,000 votes - about 6% - were disqualified for various reasons.
But according to latest official results, this figure has now come down to about 40,000. While the reason for the drop remains unclear, some observers said that election officials were being too strict first time round.
Mr Kenyatta's Jubilee coalition has rejected calls for some of these ballots to be included, as requested by Mr Odinga's allies.
Counting the rejected votes would greatly add to the number needed for a candidate to break the 50% threshold for a first-round win and increase the prospect of a runoff due within a month.
The push for these ballots to be included was motivated by a "sinister and suspect logic", said Charity Ngilu, a senior member of Mr Kenyatta's coalition.
The camp also accused the British High Commissioner in Kenya of "canvassing to have rejected votes tallied" in an attempt to deny Mr Kenyatta outright victory in Monday's vote.
The UK Foreign Office said claims of British interference were "entirely false and misleading''.
Correspondents say one of the reasons for the many rejected votes is that Kenyans had, for the first time, six ballot papers to fill in, which may have caused confusion.
The winning candidate must get more than 50% of the total votes cast and at least 25% of votes in half of the 47 counties. The latter was a requirement introduced in the new constitution to make sure the new president wins with wide support, rather than only with the backing of voters in his regional and ethnic strongholds.
If there is no clear winner, a second round of voting will take place, probably on 11 April.