Andrew Murray, who advises Mr Corbyn part-time and is chief of staff to Unite Union boss Len McCluskey, is believed to be pushing for Labour to back the Prime Minister to avoid a no-deal outcome.
The stance has provoked a furious reaction from senior Labour figures in the Shadow Cabinet, with Diane Abbott intervening to say Mr Corbyn would face protests if he supported Mrs May.
Enraged Ms Abbott turned to Mr Corbyn during a strategy meeting she organised, warning of “protests outside his house” if Labour voted with the Government, the New Statesman reported.
The Shadow Home Secretary also reportedly slapped down Mr Murray at the meeting, saying Labour’s pro-EU membership would never forgive them for aiding a “weak Tory Government”.
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A spokesman for Mr Corbyn said: “We have said very clearly we will vote down the deal if it doesn’t meet our six tests, no ifs no buts.
“Jeremy has said that if they are able to guarantee workers’ rights, and environmental protection and a permanent customs union then we could vote for their deal, but we wouldn’t vote for a bad deal.”
Mr Murray has been a key Corbyn adviser on Brexit for most of this year – assuming his role on a part-time basis for one and half days a week.
He is a prominent member of the Stop the War Coalition and a former Communist Party member.
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Centrist and pro-Remain Labour members were concerned with Mr Murray’s appointment, branding him a “Lexiteer” – a left-wing Brexit champion.
The Labour split over Brexit comes after tensions between Mr Corbyn and Shadow Chancellor John McDonnell hit fever pitch as the two MPs disagreed on how to robustly respond to Chancellor Philip Hammond’s Budget statement this week.
The next round of Budget votes are scheduled to take place on November 12 but Labour is still in disarray about how to vote.
The tensions within the Opposition were exposed even further on ITV Peston on Wednesday as Chuka Umunna refused to endorse the leadership’s plan to make its members abstain from upcoming Budget votes that disproportionately benefit the better-off.
It is understood Labour will vote down amendments to the Budget resolutions demanding a hike in income tax to 45 percent on earnings above £80,000, and 50 percent for those above £125,000.
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The expected move follows a heated row in Labour ranks after Mr McDonnell said the party would not oppose Tory tax cuts for the middle class.
Several prominent Labour MPs have called on the party to oppose the proposed changes.
But Mr Umunna did not publicly back those plans, despite Mr McDonnell suggesting the party would vote down the tax cuts.
During Prime Minister’s questions on Wednesday, Mrs May drew attention to the Labour conflict, mocking the party’s approach to tax cuts for higher earners the Chancellor announced on Monday.
She said: “We are ending austerity, we are bringing debt down, we are putting more money into our public services.”
Criticised by Mr Corbyn for choosing a “tax cut for higher earners” rather than ending a benefit freeze, she replied: “On Monday, he said cutting taxes for 32million people was frittering money away on ideological tax cuts.
“Yesterday, the Shadow Chancellor said Labour would support the tax cuts.”
On ending the benefits freeze, Mr McDonnell told ITV Peston: “We will lift the freeze and we will make sure that from then-on people get a proper cost-of-living benefit on the freeze themselves.
“What we said is that we will lift the freeze and that from then-on people will get proper cost-of-living increases.
“When we get into the next election we’ll set out our manifesto and we’ll set out a costed programme like I did last year as well.”