Mr Watson said it was clear the threat was real after a recording emerged of the founder of Momentum - the grassroots activists group which helped propel Mr Corbyn to the leadership - discussing the prospects of gaining Unite’s backing.
Jon Lansman was said to have told supporters he expected the union - together with the Communication Workers Union (CWU) - to affiliate to Momentum if Mr McCluskey wins his battle for re-election as Unite general secretary.
Warning that such a move could “destroy” Labour, Mr Watson said he would raise the matter with Mr Corbyn.
Mr Watson said he did not know if Mr Corbyn was aware of the Momentum situation.
The deputy Labour leader told the BBC Radio 4 Today programme: “They organised for him, but I’m not sure if Jeremy knows there’s a secret plan. I’ll be raising it with him today.
“I’m going to talk to him about it, I don’t know what he knows and doesn’t know.
“I’m the deputy leader and I didn’t know about it until I heard this recording. And I regard this as a battle for the future existence of the Labour Party. This is high stakes.
“What Jon Lansman has outlined is a plan with Len McCluskey, the leader of Unite, to take control of the Labour Party.”
Mr Watson said he wanted the Labour leader to “deal with” Mr Lansman.
“The significance of this is that we have never seen the biggest union organising a political faction within the Labour Party with the tacit approval of the leadership,” Mr Watson said.
Responding to initial attacks from Mr Watson, Mr Lansman said: “For 20 years the left was denied a voice. We will deny a voice to no-one. We face big challenges and we need our mass membership to win again.”
The row erupted after The Observer obtained a tape of Mr Lansman’s remarks, which were said to have been secretly recorded at a meeting of a newly-formed Momentum branch in Richmond, south-west London, earlier this month.
He is quoted as saying: “Assuming that Len McCluskey wins the general secretaryship, which I think he will, Unite will affiliate to Momentum and will fully participate in Momentum, as will the CWU.”
He went on to tell activists it was “absolutely crucial” that they secured a change to the party’s rules to ensure that whenever Mr Corbyn stands down, they are able to get a candidate on to the ballot paper to succeed him.
Currently, a candidate must obtain the support of 15% of Labour MPs and MEPs in order to stand - a threshold a new left-wing contender is unlikely to be able to achieve.
Momentum insisted there were no current plans for Unite to affiliate and said it had not received any funds from the union.
A spokesman said Mr Lansman had been speaking in “an aspirational manner” about the possibility of Unite and the CWU affiliating to Momentum.
A Unite spokesman said: “As Unite has stated, repeatedly, it is for the Unite executive council, not the general secretary, to agree to which bodies our union aligns. There are no plans whatsoever for Unite to affiliate to Momentum, as has, again, been made repeatedly clear.
“It is extraordinary that the deputy leader of the Labour Party continues to interfere in Unite’s democracy in this way.”