A row has broken out in Labour’s senior ranks after it emerged that the party was trying to use non-disclosure agreements against former staffers who contributed to what is expected to be a critical documentary about Jeremy Corbyn’s team and antisemitism.

Tom Watson, the deputy leader, said on Twitter that using expensive lawyers to try to silence former employees was “as futile as it is stupid” and he deplored the tactic.

But John McDonnell, the shadow chancellor, said the legal letters were justified. He rejected claims that Labour was being hypocritical because it had also called for the law to be changed to stop NDAs being used to gag whistleblowers.

A BBC Panorama programme to be broadcast on Wednesday, made by the veteran investigative journalist John Ware, is expected to use leaked documents and interviews with insiders to revive claims that advisers working for Corbyn intervened in antisemitism disciplinary cases in such a way as to favour some of those accused.

According to the Sunday Times, up to half a dozen former Labour staffers spoke to Panorama despite having signed NDAs with the party. Some of them have received letters from Labour’s lawyers saying they could face legal action for breaking their NDA obligations.

Charlie Falconer, the Labour former lord chancellor, said it would be “deeply wrong” and hypocritical for the party to “campaign against NDAs but use them to prevent embarrassment to Labour”. The Labour MP Wes Streeting also criticised the party for using NDAs in this way, and offered to use parliamentary privilege to disclose information on behalf of any whistleblower who felt they were being silenced.

In an interview on the BBC’s Andrew Marr Show, McDonnell said NDAs, when used properly, enabled organisations to protect confidential information, and this was what was happening in this case. He rejected Watson’s claim the party was trying to silence people speaking out about antisemitism.

Play Video 1:01 John McDonnell says Labour split stories are ‘myths and rubbish’ – video

“What is happening is that the Labour party is reminding [the former employees] of their confidentiality agreement because you can’t have people, particularly when you are dealing with individual cases, [divulging] information about individual members – that can’t be right,” McDonnell said.

He also said it may be necessary for the party to issue a fresh apology to the Jewish community for its handling of antisemitism complaints.

Asked whether he agreed with Gordon Brown, the former Labour prime minister, who in a speech on Sunday was to say the party owed Jews “an unqualified apology”, McDonnell said: “[Corbyn] made that apology. If Gordon thinks it hasn’t landed, let’s do it again, and let’s make sure that we repeat it, empathetically as well.”

He dismissed reports of a rift at the top of the party and said he had not called for Corbyn’s closest aides to be sacked. He told the Marr show: “I have confidence in them, of course I do. I have not told anyone to be sacked or anything like that, this is all myth. But let’s make it clear, Jeremy and I talk about policies on a daily basis. Yes we will disagree on things but we will then come to an agreement.”

He blamed the stories on journalists attending summer receptions and “drinking some of the most nauseating wine ever produced from a grape”.

Speaking on Sky’s Sophy Ridge on Sunday, Barry Gardiner, the shadow international trade secretary, said Labour would not use gagging orders “to hide anything that is illegal or improper” and the party remained committed to legislating to stop firms using NDAs to cover up racism, sexual abuse or illegality.

Gardiner strongly criticised the content of the Panorama programme, saying he believed it would present a biased account from staff opposed to Corbyn.

“My understanding is that it is not a balanced and objective investigation into antisemitism. It is a very partial view from a few members of staff who have a political axe to grind,” he told the programme.

Labour has been given details of the programme’s allegations, and Gardiner claimed it quoted “selectively” from internal correspondence sent about 18 months ago, when the party was in an interim period after the departure of its former general secretary, Iain McNicol, and before his successor, Jennie Formby, had fully taken over.

He said the correspondence came from former Labour officials who had asked Corbyn’s office for help in how to deal with antisemitism cases. But the programme did not make that clear, he claimed, and he said it did not feature the incidents where Corbyn’s aides proposed “a stronger response”.

In private, Labour figures have been even more critical of the BBC over the programme. One party source told the Sunday Times: “With a possible general election around the corner, this smacks of bias and interference in the political process by the BBC and a clear breach of their own editorial guidelines.”

On Sunday the BBC said Labour was “criticising a programme they have not seen”. A spokesman said the corporation was confident the film adhered to its guidelines, and that Labour had been given a chance to respond.

A Labour spokesperson said: “It appears these disaffected former officials include those who have always opposed Jeremy Corbyn’s leadership, worked to actively undermine it, and have both personal and political axes to grind. This throws into doubt their credibility as sources.

“Our records show that after these officials left and after Jennie Formby became general secretary, the rate at which antisemitism cases have been dealt with, increased fourfold.”