The A1 Darrington to Dishforth between Wakefield and the Harrogate district recorded a £132m rise, a 14 per cent increase from its original £921m budget.
Meanwhile, the M1-A1 Lofthouse to Bramham Link has got £114m more expensive.
It comes as JPIMedia revealed how the costs of 11 roads maintenance deals signed off by Highways England have swelled in price by £786m since they were agreed.
Concerns have now been raised that the escalating costs are drawing cash away from other, smaller infrastructure projects.
Among them include a campaign to transform the disused Queensbury Tunnel, between Bradford and Calderdale, West Yorkshire, into a new cycle highway.
Highways England, which is in charge of the 1.4mile-long Victorian structure, wants to abandon the route and block it off at a cost of £6m.
However, campaigners battling to protect it claim it would take just £6.9m to save the tunnel and fear the soaring costs of larger projects have doomed Queensbury.
Norah McWilliam, 71, who heads up the Queensbury Tunnel Society, said: "This is a ludicrous situation Highways England have got themselves into.
"It is absolutely baffling how many can be wasted like this. The cost of abandonment and the cost of repair have now almost closed entirely.
A spokeswoman said: "Highways England commonly works with long term contracts, and it’s normal for them to vary. These contracts include operating the roads, such as resurfacing and winter maintenance."