Transport Minister Andrew Jones said Transport for the North (TfN) would ensure a strong regional voice in decisions over major projects.
TfN is already up and running but the Government is now making moves to give it legal status.
Mr Jones, the MP for Harrogate and Knaresborough, said: “We have this stop-start approach to infrastructure development for years and we are trying to break out of that.”
He said the Government was looking at ways of taking decision-making “outside the normal parliamentary ups and downs”.
The Chancellor recently launched a new National Infrastructure Commission and suggested the North’s transport network should be one of its early priorities.
That has prompted accusations that, having already created TfN, the Government is duplicating effort and is focused on developing plans rather than delivering improvements.
Mr Jones insisted the two organisations would have different focuses but TfN would feed in advice to the infrastructure commission.
He said: “The key thing here is getting a local voice and that local voice can only come from those who know it best.
“We know transport has a fundamental role in driving economic growth and social growth and the best people who know what’s right for their area are local people.”
The Government has given TfN £30 million to develop plans including new smart ticketing across the North.