Jeremy Corbyn is on a collision course with Labour’s membership after he attempted to stop the party campaigning to remain in the EU at a general election.

Before a crucial vote on Monday on whether the party should explicitly back remain in any election, Labour’s autumn conference descended into factional rows over its Brexit policy, with rebellious MPs privately threatening another leadership challenge.

Corbyn moved to stamp his authority on Labour’s Brexit position by proposing a delay to deciding how the party should campaign at a second referendum.

His proposal to put off the decision until after an election was endorsed by the national executive committee, by 16 votes to 10, after members were asked to send their agreement by email and without a meeting.

“The NEC believes it is right that the party shall only decide how to campaign in such a referendum – through a one-day special conference, following the election of a Labour government,” the statement said.

However, pro-EU activists fought during a lengthy meeting on Sunday night to ensure there would be a vote on the conference floor on Monday on whether Labour should immediately adopt an unequivocally remain position.

More than 50 local parties swung behind a pro-remain motion, while eight backed a more neutral motion closer to the leadership’s position. Both options will now be voted on by delegates, along with the official national executive position, leaving open the possibility that competing motions could pass and cause further confusion over the party’s Brexit policy.

The pro-remain motion reads: “Labour must reflect the overwhelming view of its members and votes, who want to stay in the EU. Labour will therefore campaign energetically for a public vote and to stay in the EU in that referendum, while recognising the rights of those members who want to argue another view.”

Those close to the leadership had hoped that Corbyn’s clear statement of his position would put pressure on supportive delegates to agree a Brexit policy motion that does not contradict his view. However, party activists at the “compositing” meeting on Sunday night showed their appetite for defying the leadership over the issue of Brexit, with the aim of forcing a remain stance into the next election manifesto.

Corbyn explained he was in favour of negotiating a Labour Brexit deal before letting the party decide how it would campaign in a second referendum in an interview on the BBC’s Andrew Marr Show.

When asked if it was in Britain’s long-term interests to remain in the EU, the Labour leader suggested a Labour Brexit deal could be preferable in some circumstances: “It depends on the agreement you have with the European Union outside.”

The new position caused a fresh revolt among several shadow ministers and pro-remain activists, adding to the febrile mood at the Brighton conference following an abortive attempt by Jon Lansman, the Momentum chair, to abolish Tom Watson’s job as deputy leader and the resignation of Corbyn’s key policy aide, Andrew Fisher.

Clive Lewis, a shadow Treasury minister and supporter of Corbyn, said the leadership had been “hijacked” and was taking power away from members.

Emily Thornberry, the shadow foreign secretary, also made clear her unhappiness with the position, saying Labour risked getting stuck in a “crusher” between leave and remain with the “walls coming in” unless it picks a side before an election. She said a new direction in favour of remain needed to be decided by activists at this conference, not in a future one after an election.

Another shadow cabinet minister involved in election campaign planning told the Guardian that his position has changed and he now believes Labour needs to campaign to remain, because of the risk of voters moving to a revitalised Lib Dem party.

Many of Corbyn’s allies on the left also believe the party needs to take pick a side on Brexit before the election. Laura Parker, Momentum’s national coordinator, said Corbyn must decide on Labour’s Brexit this week, not after a general election.

“We have to decide at this conference. The one we have come to, the one we have travelled across the country to come to, not at some putative further conference which is presumably in the mythical land with that fucking table with all our options on it,” she said.

The issue has been causing serious tensions within Corbyn’s own team. It is understood Fisher, who resigned citing a lack of “professionalism, competence and human decency” in the Labour leader’s team, has been arguing that the party’s policy of trying to appeal to both sides over Brexit was no longer working and was electorally problematic.

He tweeted several supportive policy statements on Sunday, indicating he was still backing Corbyn’s project overall and sources confirmed he would stay on to write the manifesto at the next election.

Ahead of Monday’s debate, pro-remain activists were increasingly hopeful that their motion would pass, potentially with the help of some trade unions. The collective union position is the same as Corbyn’s stance, but senior union sources said Unison was considering breaking ranks.

Michael Chessum, of Another Europe is Possible, said his group had been “utterly determined” to take a remain position to conference floor and urged delegates not to see it as a test of loyalty to Corbyn.

“There will be an attempt to turn this into a loyalty test. But those proposing these motions are by and large people, like me, who have spent years fighting for the left inside Labour and backing Corbyn,” he said.

However, Len McCluskey, the general secretary of Unite, said it would be a “loyalty test” as he said any shadow cabinet ministers openly advocating a pro-remain position should get behind the leadership or “step aside”.

The second day of conference was dominated by the row over Brexit, but many anti-Corbyn MPs were also exercised by the move earlier in the week to abolish Watson’s post as deputy leader. This was abandoned on Saturday after an intervention from Corbyn, but MPs on the centrist wing of the party were up in arms about the move against him.

Several suggested on their WhatsApp group that Watson should challenge Corbyn for the leadership or lead a public split of Labour MPs, regardless of the country potentially being very close to a general election.

Watson is understood to have dismissed the idea that this was time for a breakaway but the deputy leader arrived at the party’s conference earlier than expected in order to fight any further attempts on his position.

Two shadow cabinet ministers told the Guardian they believed the bid to oust Watson was related to concerns within the Labour leadership about Corbyn’s position if he were to lose an election and stand down, with the deputy leader potentially becoming the most powerful elected person in the party.

Watson was among those on the NEC who declined to support the statement on Brexit, which is also expected to be put to a vote on the conference floor.

Watson said: “I have no doubt that Jeremy’s supporters on the NEC will endorse any statement he proposes. However, without the NEC having met to debate over it, we risk giving an imperfect document to conference, and the document not being given the weight it deserves by delegates.”