Less than 0.5% of the electorate for Labour’s leadership ballot later this month have been denied a vote, the party has announced, as it seeks to rebut claims of a deliberate purge of Jeremy Corbyn’s supporters.

The shadow chancellor, John McDonnell, has complained of a “rigged purge” of potential voters by Labour’s governing national executive committee, and Corbyn has said he would like to examine the cases of those denied a vote; while the shadow foreign secretary, Emily Thornberry, has accused senior figures of wanting to quash Corbyn’s mandate.

But the party has published figures showing that of the 650,000 people who are either already members or signed up to vote as registered supporters or trade union affiliates, a total of 3,107 have been ruled ineligible on grounds of breaches of party rules, with a further 1,616 cases still awaiting a decision.

Some applicants – including Bakers’ Union boss Ronnie Draper – have complained about being excluded on the grounds of past comments made on social media, with no details provided about the precise nature of the offence.

But a party spokesperson said: “The Labour party has a robust validation process for all votes in this year’s leadership contest to ensure every vote cast is eligible according to the party’s rules and agreed procedures.

“The speculation that huge numbers of applicants have been denied a vote has been wildly exaggerated.”

A detailed breakdown showed that 1,634 had been ruled ineligible by the NEC panels set up to judge cases of party rules being breached.

The rules for the contest state: “No abuse of any kind by members or supporters shall be tolerated. All eligible members and supporters must conduct themselves in a calm and polite manner and be respectful to each other at all times. Behaviour including, but not limited to, racist, abusive or foul language, abuse against women, homophobia or antisemitism at meetings, on social media or in any other context will be dealt with according to the rules and procedures of the Labour party.”

About half of the cases referred to the NEC panels for a decision were rejected, the party said. In addition, 990 people have been excluded because they admitted being a member of another party and another 434 because they have previously nominated a rival political candidate.

Separately, more than 21,000 applicants did not provide details that matched the electoral roll. In another 3,791 cases, the £25 payment necessary to register as a supporter failed.

The bitter tone of the leadership election campaign has raised fears about the difficulty of reuniting Labour after the results of the contest are announced on 24 September, on the eve of the party’s annual conference in Liverpool.

Corbyn’s team have suggested that plans for a closer working relationship between the leader’s office, the shadow cabinet and the parliamentary Labour party will be announced in the run-up to the poll. He will face his challenger, Owen Smith, in a special BBC Question Time programme on Thursday night.

Smith has accused Corbyn of being a “disunity candidate”, saying he has failed on a series of occasions to tackle personal abuse and accusing him of appearing to sanction the threat of deselection against rebellious backbenchers.

“By failing to act against abuse, attacking party staff and the NEC and encouraging talk of deselection, Jeremy has shown that he is both unwilling and unable to act as a unifying figure. That’s not the leadership the Labour party needs – it’s not leadership at all.

“He says he wants to build bridges, but the truth is he appears more interested in deepening the divides within the party than winning elections,” Smith said.]

The PLP has backed a proposal for the restoration of elections to shadow cabinet positions – a convention ended by Ed Miliband. But Corbyn’s allies suggest that idea would only be acceptable as part of a package of measures to “democratise” Labour, which would also involve grassroots members more closely in decision-making, and would have to be passed by conference.

Corbyn and Smith have each held scores of rallies up and down the country, and faced each other at a number of increasingly ill-tempered hustings events.

As well as questioning Corbyn’s competence as a leader, Smith has clashed with him on a series of policy issues including the Trident nuclear deterrent and Britain’s future relationship with the EU.

The leadership contest was triggered after Corbyn faced a series of resignations from his frontbench team in the wake of Britain’s vote to leave the EU. His critics in the PLP accused him of failing to argue vigorously for a remain vote and of a shambolic leadership style but he is widely expected to win the contest, in which members have the final say.

The early stages of the leadership race were marred by high court battles about whether Corbyn’s name should appear automatically on the ballot paper, without having to muster nominations among MPs; and whether the NEC could impose a six-month cutoff date on new members hoping to vote.

Tom Watson, Corbyn’s deputy, also sparked a row by claiming the party was at risk of being infiltrated by “Trotskyist entryists” seeking to capitalise on his leadership.