Minister Chris Heaton-Harris said Department for Transport civil servants had been working with local leaders and metro mayors to identify the projects and were now "trying to get money out of the Treasury".
He cited the upgrade to the Hope Valley rail line between Sheffield and Manchester, which the Government announced last week would be getting £137m of investment, as an example of how the new body would work.
But he insisted that despite the creation of a new northern transport body there was still an important role for Transport for the North, which has had its budget cut amid fears it is being sidelined by the Government.
The North Transport Acceleration Council (NTAC) was announced last summer by Mr Shapps, who has previously described TfN as "by definition a talking shop".
Mr Shapps, who is also the Northern Powerhouse Minister, chairs NTAC and says it gives northern leaders a "direct line" to Ministers to speed up the delivery of projects.
TfN, which relies on central government for funding, is jointly responsible with the Department for Transport for delivering the flagship Northern Powerhouse Rail scheme but does not have the power to instruct other agencies on projects.
It emerged this week that the Department for Transport is creating a 'northern hub' with hundreds of civil servants in Leeds.
But Rail Minister Chris Heaton-Harris rejected the idea that this meant DfT would be taking over some of the functions of TfN.
He said: "TfN provides quite an important link for me, Grant and officials in proper structured dialogue with local authorities, combined authorities, mayors.
"There is a distinct purpose to the acceleration council because we do want to get on delivery of these schemes.
"A very good example of this is that we have identified over 100 schemes that we know that working together we can speed up, we're trying to get money out of the Treasury to make sure we can do these sorts of things.
"There was an example of that only last week, where over £130 million pounds got released for the Hope Valley engineering works which really will be a game changer for reliability of services as you head across to Manchester.
"So there is absolutely purpose to it, I'd like to think maybe those conversations could be more enriching, and possibly done post pandemic over coffee and in person rather than via calls and stuff but I don't see there being any replacement."
A DfT spokesperson said: “We are investing billions to level-up infrastructure across the North, and the Northern Transport Acceleration Council will be crucial to ensuring improvements are made as quickly as possible.
“We continue to work closely with Northern leaders to identify local priorities and will be holding the next NTAC meeting this month.”