Critics say the Labour leader is making his party a “laughing stock” by stopping MPs and working class supporters from having their say.
Momentum used a new app that whipped its supporters to stop Brexit policy being voted on in order to avoid a potentially embarassing result on staying in the single market.
It meant an effort to have the issue of immigration after Britain leaves the bloc was ditched in favour of debates on things like social care and the NHS.
Outraged senior Labour figures have accused Mr Corbyn of avoiding the most important issue facing the country.
Former spin doctor Alastair Campbell lashed out on Twitter, writing: “Are we seriously saying that a 'government in waiting' isn't debating Brexit at its Party Conference? If so, not serious.”
And form shadow cabinet member Heidi Alexander fumed: “I am gobsmacked.
“How can @uklabour not have a full & proper debate on Brexit policy at #Lab17?
“We will be a laughing stock.”MP Pat McFadden agreed, tweeting: “Labour must debate the biggest issue facing the country.”
Backbencher Alison McGovern told a rally organised by the Blairite Progress group she was "gutted" that there would not be a vote on Brexit at the conference.
A motion by the TSSA union calling for the party to veto any Brexit deal that ended free movement was also blocked.
One member of the union told the Financial Times: “Jeremy stood on a platform of giving the party back to the members, but it appears his team are tone deaf as this has not got through to them.”
Mayor of London Sadiq Khan also weighed in, saying: “We must fight to protect workers’ rights, stay in the single market and maintain the ability to attract talent from Europe and around the world.
“Throughout our history, we’ve always been open to the world and open to people.”
Although delegates will discuss Brexit on the conference floor today, there will be no vote.
But John McDonnell this morning denied that Labour's leadership was trying to quash debate about Brexit.
The shadow chancellor insisted there would be "plenty" of debate on the party's stance on EU withdrawal, with delegates on Monday discussing a report from the leadership being presented by shadow Brexit secretary Sir Keir Starmer.
Asked whether the leadership was trying to dodge scrutiny of its position, the shadow chancellor told ITV1's Good Morning Britain: "I wouldn't characterise it that way.
"In our new politics, we are saying conference needs to be controlled by the delegates. They decide what we will debate, not the leadership.
"This is democracy at work."
Delegates were free to reject the leadership report if they chose, said Mr McDonnell.
But he added that he believed the decision not to prioritise Brexit for debate was motivated by "a feeling that there needs to be a bit more consensus-building, rather than dividing the party at the moment".
Mr Corbyn is resisting pressure from europhiles in the party, who want him to commit Labour to keeping the UK permanently in the European single market and customs union after Brexit.
Shadow Brexit secretary Sir Keir Starmer has previously said that under a Labour government Britain would remain in both for a transitional period of two to four years after the official Brexit date in 2019.
But signatories to a letter published in the Observer, including former shadow cabinet members Chuka Umunna and Heidi Alexander, said the party should go further to protect jobs and workers' rights.
Liberal Democrat shadow Brexit secretary Tom Brake said: "Corbyn's anti-EU wing of the Labour party have won the day.
"Following pressure from his Momentum pressure group the party have ducked away from debating the biggest issue currently facing the country at their conference.
"Labour have again shown themselves to be neither here nor there, unable to come up with a coherent policy for fear of their own internal politics spilling out into the public. Labour do not stand for anyone on Europe."