John McDonnell has rejected warnings from Len McCluskey, the Unite leader, that Labour members would see support for a second Brexit referendum as a betrayal, adding that in a choice between Theresa May’s deal and staying in the EU he would vote remain.

McCluskey, who wields substantial influence in the party, told a group of Labour MPs this week that they could alienate supporters by backing a fresh referendum, and urged them to stick to Labour’s alternative Brexit plan.

Asked during a visit to Glasgow on Friday whether he agreed with McCluskey, McDonnell said: “No.”

The shadow chancellor said if there were a second referendum it was “inevitable” that the choice for voters would be remain versus Theresa May’s deal, adding: “And if it was, I would vote remain.”

He said: “I think if we get to a situation where we’d tried everything and we have tried everything … We’re doing our best. My speech yesterday [in the Commons] was a sincere attempt to try and bring all parties together to try and agree a Brexit which will protect jobs and the economy.

“If we can’t get that, we need a general election because we can then change the team that will then do the negotiations. If we can’t do that, well, I think people will recognise we have no other option but to consider another public vote and people will respect us for doing our best to implement the spirit of the referendum.

“We’ve got to resolve this issue. We can’t go on like this.”

Speaking at the start of a two-day visit to Scotland, McDonnell said Labour would make concerted attempts to win majority support for its Brexit strategy once May’s deal was rejected next Tuesday.

He said the party would “plant a flag” for its counter-proposal to see which other parties and which disillusioned Tory MPs were willing to rally around it, but acknowledged Labour could fail to win enough support.

He dismissed repeated warnings from the European commission that May’s deal could not be renegotiated. Pointing to the Irish referendums over the Lisbon treaty in 2008 and 2009, and other EU members’ referendums on treaty proposals, he said the commission had delayed agreements and redrafted treaties in the past when it was expedient.

It remained possible that an alternative Brexit deal could be put forward and negotiated before the current article 50 deadline of 29 March, so it was not necessarily inevitable an extension to that would be required, he said.

“We can still do a deal [by 29 March], we can still do that … but yes, you’re right, as time moves on it makes it that much more difficult and of course the extension of article 50 is available to us.

“The climate will change. That will change. Look what happened over Lisbon. That changed rapidly. They’ve watched what’s happened in the UK parliament, haven’t they? And they’ve seen the disarray that this government is in.

“It’s a deal that they’ve signed up reluctantly themselves. They’ve seen this deal isn’t going to work, so therefore other opportunities will have to be explored. And they want the best optimum solution that will protect the European economy overall, just as we wish to protect the UK economy.”