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Building Northern Powerhouse Rail (NPR) risks repeating the failures of HS2 with “no convincing plan” to deliver it within a £45bn budget, an influential committee of MPs has warned.

The government announced in January its commitment and funding for the NPR project to connect cities across the north, consisting of new or upgraded lines between Liverpool, Manchester, Leeds, York and Sheffield.

However, a report from the public accounts committee (PAC) said it was not confident that the Department for Transport had “learned all the lessons from its past failures in its management of other rail projects” and said there were “clear risks that the full programme and benefits cannot be delivered within its £45bn funding cap”.

High-level plans for a transformed railway across the north were first announced in 2014, and promised by successive Conservative prime ministers. While the latest iteration of NPR, a three-phase plan building on the current TransPennine Route upgrade work, has more detail, the committee said there was “considerable uncertainty still clouding the project”, including journey times, capacity, the exact routes, and who will build the new lines.

The committee said it was “unclear how HM Treasury determined the £45bn cap before the entire project is designed, scoped and costed”.

The report warned that the final phase of NPR, a new Liverpool-Manchester line, would be at risk if the DfT could not scope the programme within the cap or if the estimates proved unrealistic.

It added: “This serious risk is heightened by HS2 Ltd’s responsibility for producing some of the cost estimates and the department’s poor record on rail infrastructure costs and cost estimation.”

One unresolved question concerns whether a new station is built underground at Manchester Piccadilly, which Andy Burnham has long demanded as mayor, but according to some estimates could cost £5bn more than a surface station.

Clive Betts, deputy chair of the PAC, said there was “an appetite to finally deliver the transport infrastructure the north so badly needs”.

But, he added: “The spectre of HS2 hangs over Northern Powerhouse Rail. Our committee has heard troubling echoes of the same mistakes in loose governance that HS2 made early on … As HS2 has been a casebook example of how not to run a major project, so their involvement in NPR does not fill us with confidence.

“Both the Treasury and DfT have questions to answer about the project’s £45bn funding cap. Given the fact that this project has not been fully scoped or designed, it is hard to see how the government was able to arrive at a hard £45bn cap. We need to know how this figure was arrived at and how DfT will keep to it.”

He added: “We also need to understand how mayoral authorities will have enough scrutiny for this project to be delivered successfully.”

A Department for Transport spokesperson said: “Northern Powerhouse Rail will deliver the biggest investment in rail connectivity in a generation, giving the north the transport links it deserves and driving growth, jobs and investment across the region.

“NPR will not repeat the mistakes of HS2 which is why we accepted all the recommendations of the James Stewart Review and are taking a disciplined, phased approach – completing detailed technical work with all stakeholders before fixing precise choices for major infrastructure.”

Henri Murison, the chief executive of the Northern Powerhouse Partnership, said that while the government had set out high-level scope and timings for the railway, “we now need clarity on key issues”.

He said that Burnham’s new “No 10 North “would play an essential role in directing officials, adding: “The Treasury must also ensure the necessary fiscal devolution is in place to allow funding to be raised for Manchester Piccadilly underground station and other key elements of the programme. We expect to see serious progress in the autumn budget.”