Eight people told Panorama they were undermined in their attempts to tackle anti-Jewish abuse in the party.
Former officials alleged that Labour's director of communications, Seumas Milne, and its general secretary, Jennie Formby, interfered with investigations.
Four of those who spoke out, including former Labour general secretary Iain McNicol, broke non-disclosure agreements to do so.
Reacting to the revelations, senior party figures in the region expressed their support for the Jewish community and called for change.
Leeds Central MP Hilary Benn tweeted: “Following last night’s Panorama, as Labour Party members we should ask ourselves this question.
“Why do the young Jewish members who bravely spoke out feel so unwelcome in our Party? Until they say things have changed, we will not have dealt with the problem.”
Leeds West MP Rachel Reeves, said: “I’m proud to be a member of the Jewish Labour Movement. Join in solidarity with our Jewish members - without them our party is incomplete.”
And Hull North MP Diana Johnson posted a quote about the holocaust which read: “Remember, it didn’t start with gas chambers. It started with politicians dividing people with “us vs.them”. It started with intolerance and hate speech and when people stopped caring, became desensitized and turned a blind eye.”
However, others accused the programme makers of bias against Labour, with Huddersfield MP Barry Sheerman tweeting: “In my view as someone who is totally committed to eradicating anti-semitism in our Labour Party last nights BBC programme was unfair & unbalanced.”
Responding to the programme, a Labour spokesman said the party rejected any claim it is anti-Semitic and said it 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 stand in solidarity with Jewish people, and we're taking decisive action to root out anti-Semitism 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," the spokesman said.
"Despite claims made in the programme, Labour is taking decisive action against anti-Semitism. Since Jennie Formby became general secretary the rate at which anti-Semitism cases have been dealt with has increased more than four-fold."