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.”
Deputy leader Tom Watson tweeted: "I am shocked, chilled and appalled by what I’ve just seen on Panorama. Hearing the testimony of party members and former staff was harrowing. They are not “disaffected”, they have been incredibly brave. Very serious questions now have to be answered."
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.
In a statement after broadcast, it said:“We completely reject any claim that Labour is antisemitic. We stand in solidarity with Jewish people, and we’re taking decisive action to root out antisemitism from our movement and society.
“The Panorama programme was not a fair or balanced investigation. It was a seriously inaccurate, politically one-sided polemic, which breached basic journalistic standards, invented quotes and edited emails to change their meaning. It was an overtly biased intervention by the BBC in party political controversy.
“An honest investigation into antisemitism in Labour and wider society is in the public interest. The Panorama team instead pre-determined an answer to the question posed by the programme’s title.
“No proper and serious attempt was made to understand our current procedures for dealing with antisemitism, which is clearly essential to reach a fair and balanced judgement. And Panorama distorted and manipulated the truth and misrepresented evidence to present a biased and selective account.
“We complained in advance to the BBC over the way the programme was put together and its choice of a presenter who has expressed overt personal and political hostility to Jeremy Corbyn’s politics. We will be pursuing complaints at every level.
“The Labour Party will fully investigate any complaints concerning the antisemitic incidents reported by party members in interviews in the programme.
“Labour stands in solidarity with Jewish people and is fully committed to the support, defence and celebration of the Jewish community and its organisations.
“Despite claims made in the programme, Labour is taking decisive action against antisemitism. Since Jennie Formby became General Secretary the rate at which antisemitism cases have been dealt with has increased more than four-fold.
“We will build on the improvements to our procedures made under Jennie Formby, and continue to act against this repugnant form of racism.”