Conservative frontbencher Andrew Stephenson was asked by Labour's Grahame Morris (Easington) to correct the Prime Minister's previous denial over Transport for the North suffering a 40 per cent budget cut.
Mr Stephenson replied: "The honourable gentleman has been in this House long enough to know that the Prime Minister is always right."
Sir Lindsay intervened and said: "You might be proved wrong."
Mr Johnson claimed there has been "no such cut" to Transport for the North's budget when challenged about it last month during Prime Minister's Questions.
Hull MP Dame Diana Johnson asked in the Commons: “Is the 40% cut to Transport for the North’s budget part of the Prime Minister’s plan for levelling up the North?”
The Prime Minister replied: “There has been no such cut, we intend to invest massively in northern powerhouse rail, in railways in the North and across the entire country.”
Board papers for the transport body, which aims to boost connectivity in the North of England, said core funding from the Government would drop from £10 million in 2020/21 to £6 million in 2021/22. But when other funding streams, such as the money available to develop Northern Powerhouse Rail, are taken into account the cut is less than 40 per cent.
There are concerns that Transport for the North is being sidelined by Ministers as Transport Secretary Grant Shapps has set up his own 'acceleration council' to make quicker progress on big infrastructure schemes.
The strategic body, which took on statutory powers in 2017, was created with the aim of transforming northern transport links but is reliant on central government for funding.
The Prime Minister was also accused of lying to MPs at PMQs this week by incorrectly claiming that Labour voted against an NHS funding package.
In January, shadow transport secretary Jim McMahon also accused Mr Johnson of "misleading" MPs by claiming his 200-day-old comments on quarantine measures were recent.