The Panorama investigation, broadcast on Wednesday, featured claims from ex-party officials that senior Labour figures had interfered in the disciplinary process of dealing with accusations of anti-Semitism.
A total of eight former Labour officials spoke to Panorama, including Dan Hogan, who was an investigator in the disputes team, and made accusations about Jennie Formby.
Fiona Sharpe, spokesman for Labour Against Antisemitism, said in a statement, "Tonight's hour-long special edition of Panorama asked the question 'Is Labour Anti-Semitic?' The answer conclusively is yes - from the very top of the organization downwards".
Ms Formby said she was "very concerned" by the distress suffered by some former staff members shown in the Panorama documentary, but added that "we were not made aware of these issues at the time". As described by Jewish NEC member Jon Lansman, on resigning they stole and then deleted whole tranches of correspondence - so that once again the Party could be blamed for not processing allegations effectively.
Earlier, Mr Watson said the party had failed to address the "permissive culture" that people can use anti-Semitic language in meetings and on social media.
Many are the result of bulk allegations generated on an industrial scale by just a few organisations, prominent among them the Campaign Against Antisemitism, and Labour Against Antisemitism, set up explicitly to undermine the Corbyn leadership and to protect Israel.
"There's nearly a permissive culture that people can use anti-Jewish, racist language both in our meetings and to each other on social media and we've failed to address that properly", Watson told BBC radio.
"It does seem to me that there is obviously some participation in these disciplinary cases from the leader's office, which means they are responsible for dealing with the rebuilding of trust in the Jewish community".
Numerous team claimed their mental health had been damaged by the attitude of senior members of Jeremy Corbyn's team.
The programme adhered to the BBC's editorial guidelines, including a full right of reply for the Labour Party.
"It must have taken great courage for them to whistleblow and for them to have to call out our core practices I think is deeply sad - and actually deplorable that we would just dismiss them as in some way sort of disaffected", he said.
He added: "We've got to be much stronger in saying denying the problem, is part of the problem".
In a statement, the United Kingdom -based Campaign Against Antisemitism (CAA) said the BBC exposed what the group had been saying about the party and its leader.
One member said, "I joined the Labour party because of my Jewish values" but had "been the unfortunate victim of a lot of antisemitism within the Labour party, and stuff I never thought I'd receive in 2019, let alone in the party I thought was anti-racism".
Joshua Garfield, a Labour councillor in Newham East London, who appeared in the documentary responded that: "I think that that is, frankly an outrageous thing to say".
Labour's deputy leader Tom Watson, who has been critical of Corbyn, said the revelations were "harrowing".
"Whether he himself is an anti-Semite or not is an irrelevance".
The Labour Party must move to a fully independent complaints procedure, free from political interference from Jeremy Corbyn and Jennie Formby.
A Labour spokesman told Sky News "we stand in solidarity with Jewish people".
It also accused the Panorama programme of being a "seriously inaccurate, politically one-sided polemic, which breached basic journalistic standards, invented quotes and edited emails to change their meaning".
"This unprecedented exposé of a political party seemingly steeped in institutional racism has uncovered a Labour elite who have, it is alleged, consistently lied to the British Jewish community and to the British electorate", she continued.