Mr Barclay said a "constitutional collision" in a series of ‘indicative votes’ on alternative Brexit plans could result in a snap vote.
A series of votes on up to seven different Brexit outcomes - including revoking Article 50 entirely or holding a second EU referendum - are expected by Wednesday this week, with backbenchers and government ministers proposing them as a solution to the deadlock.
"And that is something that Brexiteers like me would see as a massive risk to Brexit because if Brexiteers and Parliament votes against the deal and also votes to take no-deal off the table then the only option is to then have European parliamentary elections."
Mr Barclay said if the Commons takes control of the order paper and votes for a different outcome, it would "potentially collide with fundamental commitments the Government has given in their manifesto", though he said the vote itself would "not be binding".
Explaining the scenario, he said: "What Parliament has done is vote for a number of contradictory things so we would need to untangle that but ultimately, at its logical conclusion, the risk of a general election increases because you potentially have a situation where Parliament is instructing the executive to do something that is counter to what it was elected to do."
Earlier, Philip Hammond became the first Cabinet minister to suggest a second EU referendum could go ahead, describing it as a “perfectly coherent position” which should be considered in indicative votes.
"One way or another Parliament is going to have the opportunity this week to decide what it is in favour of, and I hope that it will take that opportunity - if it can't get behind the Prime Minister's deal - to say clearly and unambiguously what it can get behind," the Chancellor said.
After hundreds of thousands of people descended on Parliament on Saturday demanding a so-called People's Vote, he said a second referendum was a "perfectly coherent position" which "deserves to be considered along with the other proposals".