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.”

Councillors on Shetland have backed plans to build up to four tunnels to link some of the largest and most populated islands, after years of isolation and decline.

The council voted on Tuesday to investigate financing options for the first two subsea tunnels, which would link Shetland’s Mainland with the two large northerly islands of Yell and Unst.

Islanders on Yell and Unst have campaigned for years for fixed links to replace their ageing and unreliable ferries, after witnessing families leaving, businesses closing and parents forced to live away from home for work.

The two projects, the first of their kind in Scotland, will cost about £655m to build and take at least eight years to complete.

Emma Macdonald, the leader of Shetland Islands council, said it would press the Scottish and UK governments for help with the construction costs, which were unaffordable for Shetland on its own.

“Islands with fixed links repopulate, enjoy economic growth and experience a reduction in their average age,” Macdonald said. “We have no ‘do nothing’ options here. Ferries and tunnels are both needed to unlock the potential of Shetland, and both the Scottish and UK governments have a vested interest in helping that happen.”

The archipelago’s roll-on, roll-off ferries are more than 32 years old on average. They have struggled to recruit and retain staff; 50% of their crew are aged 46 or over. They stop operating overnight, have limited capacity and are routinely unable to sail due to bad weather, while facing soaring repair and replacement costs.

For many islanders, that dependency increases the sense of insecurity and isolation, and drives depopulation. Relatively short journeys can last hours.

Shetlanders often look enviously at their near neighbours in the Danish-speaking Faroes, where its tunnels, including the world’s only undersea roundabout, offer seamless connections, and the Norwegian islands linked by tunnel to the mainland.

Councillors hope to persuade Scottish and UK ministers to provide some of the core funding, either through the Scottish National Investment Bank or national wealth fund, by arguing that the islands are an essential part of the wider UK economy.

The UK’s only space port at SaxaVord on the far northern tip of Unst is due to host its first rocket launches later this year, and Shetland produces 22% of Scotland’s farmed salmon and 88% of its farmed mussels, while its trawlers land seafood valued at £147m.

Engineering consultants calculated the road tunnel between Mainland and Yell would cost about £352m to dig, with operating costs of £90m over the next 60 years.

The tunnel linking Yell with Unst would cost about £300m, with running costs of £72m. Those costs would partly be met by tolls and could be part-financed by private investors who could then run the tunnels.

In turn, each would generate tens of millions of pounds in growth, and improve the islands’ social and economic resilience, the council said. Official data shows the population has fallen by 24% in the last 40 years.

Councillors also agreed on Tuesday that tunnels could be built later to link two smaller islands that sit east of Mainland – Bressay and Whalsay, with new ferries proposed for the outlying islands of Papa Stour and Skerries.

If Shetland’s tunnels are funded, their construction is expected to reinvigorate calls for subsea tunnels or bridges in the Western Isles, which are also heavily dependent on ferries.

Orkney Islands council argues that its geography makes tunnels and bridges less significant; some islands are already connected to mainland Orkney by fixed links known as the Churchill barriers.

Alice Mathewson, a spokesperson for Yell and Unst tunnel action groups, said the tunnels would be financially viable, and lower carbon than the ferries. “These links will not only bridge geographical divides but also enhance the prosperity and wellbeing of our island communities,” she said.

The Scottish government has been approached for a response.

A herd of cows has disrupted travel for thousands of train passengers after wandering on to Britain’s busiest intercity railway line.

Trains between London and Manchester were among those cancelled, with delays and disruptions affecting multiple train services on Tuesday after the errant cows blocked the west coast mainline in Staffordshire for more than three hours.

The cow incursion, which occurred shortly before 9am, was expected to affect services until 4pm, with delays and cancellations for Avanti West Coast and Lumo services between London Euston and Scotland, as well as London Northwestern and West Midlands trains.

Tickets are being accepted on certain alternative routes.

The incident blocked the line between London and Manchester a day after the prime minister-apparent, Andy Burnham, announced plans for No 10 operations split between the two cities – undeterred by his late arrival in Westminster last week on another delayed Avanti train, in a separate, non-cow incident.

According to the Press Association, railway staff had difficulties contacting the farmer responsible for the animals to move them off the track.

Burnham has called for the UK to be “able to take greater public control” of transport, but it is unclear if this is the kind of control he had in mind.