Senior Labour figures have been accused of interfering with the disciplinary process investigating claims of anti-Semitism, according to BBC Panorama.
In a programme to air on Wednesday night, communications chief and Jeremy Corbyn ally Seumas Milne and National Constitution Committee general secretary Jennie Formby are singled out for criticism.
Labour has denied the claims and written a complaint to the BBC.
A total of eight former Labour officials spoke to Panorama, including four who have signed non-disclosure agreements (NDAs) on the subject of anti-Semitism, according to the BBC.
Dan Hogan, who was an investigator in the disputes team, raised issues about Ms Formby.
He alleged people she had brought in since her appointment "overruled us and downgraded what should've been a suspension to just an investigation or worse to just a reminder of conduct, effectively a slap on the wrist".
Former head of disputes Sam Matthews said he interpreted an email from Mr Milne as "not a helpful suggestion" but as "an instruction".
The BBC reports that, in the email from March last year, Mr Milne said there should be a review of the disciplinary process into anti-Semitic complaints.
"Something's going wrong and we're muddling up political disputes with racism," he reportedly wrote.
"I think going forward we need to review where and how we're drawing the line."
Anti-Semitism complaints within the party have increased significantly since Mr Corbyn became leader in 2015, the broadcast suggests.
The BBC is yet to release any numbers in relation to the complaints.
The investigation details allegations the complaints process had interference from within the Labour leader's office.
Testimony reportedly includes allegations there were substantial disagreements within the party about what constituted anti-Semitism.
It features a claim complaints were processed directly by aides in Mr Corbyn's Westminster office on one occasion, the broadcaster said.
Labour, which has been braced for the accusations, wrote to BBC director-general Lord Hall to complain ahead of the broadcast.
"We've had a number of questions put to us by the Panorama team and we've answered them fully and extensively," a Labour source said.
"And from what we've seen of the questions and the nature of the investigation, the Panorama team had already come to a conclusion about where its investigation was going before it looked at the evidence in full.
"We are absolutely adamantly opposed to anti-Semitism in all its forms and we will continue to take the strongest action to eradicate it from the Labour Party, and we've taken a series of steps."
A BBC spokesman accused Labour of "criticising a programme they have not seen".
He said: "The programme adheres to the BBC's editorial guidelines.
"In line with those, the Labour Party has been given the opportunity to respond to the allegations."