The decision will be a major disappointment for Mr McCluskey, who had been confident of getting their endorsement.
One senior Unite source told PoliticsHome: “Len had been openly stating at officer meetings that Unite Now would endorse him, so this is a bitter blow.
“Unite Now members mainly work in aerospace, shipbuilding, engineering, energy, automotive and nuclear, which all have a lot of membership in large blocks.
“They very well organised and came out in support of McCluskey in the last two elections.”
The general secretary election was called when Mr McCluskey dramatically resigned last month. His term of office was due to run until 2018.
He has said he wanted to save the union money by holding the ballot at the same time as elections to Unite’s executive council, which take place in the spring.
Mr McCluskey is being challenged by Gerard Coyne, Unite’s regional secretary in the West Midlands, and left-wing candidate Ian Allinson.
The contest has already turned ugly, with Mr Coyne accusing his rival of being Jeremy Corbyn’s “puppet master”.
In return, Mr McCluskey has accused Mr Coyne of being the representative of the MPs who were behind last year’s failed attempt to oust the Labour leader.
In their statement, Unite Now – which is mainly made up of former members of Amicus, which merged with the Transport and General Workers Union to form Unite in 2007 – said: “After extensive debate at a national meeting, Unite Now have decided that at this present time, we will not endorse any of the candidates in the upcoming general secretary election.
“We believe that the election of the executive council of the union is of more importance, this is something that appears to be losing focus since the announcement of the general secretary election.
“The executive council is the supreme decision body of our union and it can, and must, hold the general secretary to account – regardless of who is actually elected.
Mr McCluskey said: “As this campaign continues, members will see that I am the only candidate with the experience, the track record and the vision to protect their jobs and living standards. I am confident that I will attract the support of many individual Unite Now members as the campaign unfolds.
“Ours is a proudly democratic union. I am determined to uphold that democracy, especially now as a threat to our independence emerges from those supporting one candidate. We must defend our traditions and protect our union from being used as a proxy for internal battles by failed elements within the Labour party.”
Mr Coyne said: “This is very significant that a group of lay activists who have historically supported Len are not mandating their members, many of whom I know are supporting me. I’m very pleased.”