A substantial discrepancy in the final ballot count at the Conservative leadership convention is threatening to spill into open revolt and undermine the electoral legitimacy of new leader Andrew Scheer.

Followers of Maxime Bernier are raising alarm bells about the gap between the votes cast and the final number announced at last weekend's convention, where Mr. Scheer won a razor-thin victory over Mr. Bernier.

"Obviously it is concerning, but I am hoping that the party is working very hard to provide a satisfactory answer to the candidates and the party," Conservative MP Tony Clement, a key player in the Bernier leadership team, told The Globe and Mail on Friday.

Story continues below advertisement

Barrie McKenna: Andrew Scheer's economic plan for Canada remains a mystery

Read more: How Maxime Bernier lost and Andrew Scheer won the Conservative leadership

A Conservative Party whistleblower is expected to come forward on Monday with a sworn affidavit, detailing troubling questions about the results of the final vote, a member of the Bernier team told The Globe.

The dispute could jeopardize Mr. Scheer's hold on the party leadership if Mr. Bernier – who has a large following among Conservatives – decides to publicly challenge the results. It may also be an indication that Mr. Bernier will not play the role of loyal soldier.

The Conservative Party says 141,362 voters were counted last Saturday, but the strikeout list sent to all the campaigns appear to show 133,896 votes tallied. There were 10,429 spoiled or incomplete ballots.

The Bernier camp wants to know why party director Dustin van Vugt ordered that all the ballots be destroyed immediately after the vote and why scrutineers were also not informed that there was a 7,466 vote discrepancy. Only 7,049 votes separated the two candidates on the final ballot.

"There are deep concerns that there are more than 7,000 more ballots in the ballot box than there were supposed to be, which is a big problem," another senior Bernier adviser said, speaking on background. "Something went horribly wrong. That decision to destroy the ballots and not inform the scrutineers is a terrible decision."

Story continues below advertisement

Conservative Party president Scott Lamb said the election was fair and the results stand.

"Elections are decided and verified and complete, and people can speculate about them all they want. But it was an audited, final result," he said in an interview. "I think it's a distraction to a good and fair process and it's just unfortunate these sort of things go on where people are confused about some numbers and discrepancies that have nothing to do with the actual vote."

Officials at Conservative Party headquarters are downplaying the seriousness of the Bernier team's allegations, noting they are coming from a losing camp in a lengthy, hard-fought campaign.

"The story is there are some people who are mad," one party official said, speaking on background. "They thought they won and they had it taken away, and they're really angry."

The party official said the discrepancy is due to the fact that the names of about 3,000 people who voted at 13 polling stations outside of Toronto weren't entered into the party's database and therefore weren't on the list provided to campaigns the night before the vote.

The official said the other issue is inconsistent data entry on about 4,000 ballots – a result of volunteers having to go through more than 140,000 ballots in a short period of time.

Story continues below advertisement

The party president said ballots were watched and verified from start to finish by both party scrutineers and auditing firm Deloitte. The ballots were kept in a locked room on a 24-hour webcam and transported in a locked Brink's truck from Deloitte in Vaughan, Ont., to the Toronto Congress Centre, where the vote was announced.

"The integrity of the process for the ballots and the vote were scrupulously followed according to the rules for the leadership race," Mr. Lamb said. "The campaigns had scrutineers present at all times. Our auditors, Deloitte, verified and confirmed the result."

Mr. Scheer's office declined to comment on the allegations, calling them a party matter. "The party runs the show. So this is a question for the party," spokesman Marc-André Leclerc said.

The Bernier team said almost 7,500 votes is not a small discrepancy and they want to be able to talk to Deloitte about what happened.

The Conservative Party said there is, however, a digital image of every ballot cast and claim if the votes were re-counted it would elicit the same result.

Mr. Scheer edged out Mr. Bernier, the front-runner, by less than two percentage points on the 13th and final ballot, finishing with 50.95 per cent of the vote.

Story continues below advertisement

Meanwhile, the National Firearms Association obtained the Conservative Party membership list and sent out flyers selling memberships to the gun lobby group.

The Conservative Party plans to issue a cease and desist letter to the organization and demand it destroy the list. The membership list is traceable, so the party already knows which leadership candidate leaked the list.

"We've passed along all information regarding this to our chief returning officer to make a ruling on what we believe is a violation of the use of the membership list we supplied to leadership campaigns," party spokesman Cory Hann said. He did not specify what the punishment might be for breaking the rules.