The Gateway project to build two new badly needed tunnels for trains under the Hudson River is already running two years behind schedule — even though it just broke ground, a federal audit shows.

Officials at the Gateway Development Commission have publicly stated that by 2038 they will have finished digging and constructing the new tunnels and then rehabilitate the two existing trans-Hudson tubes, which were badly damaged by Superstorm Sandy.

However, the audit performed for the U.S. Department of Transportation’s Transit Administration shows the work will likely take until 2040.

The audit revealed that the biggest tasks the agency faces include staffing up, awarding massive contracts and the need to do substantial prep work because of the complicated Hudson River geography. If this doesn’t happen soon, the project could fall even further behind.

“If GDC cannot reach the necessary level of capacity and capability to effectively execute the work according to the 18-month staffing plan, it could result in significant delays to the schedule and additional cost,” the review warned.

U.S. Sen. Chuck Schumer speaks at the groundbreaking for the Gateway tunnel on the Manhattan side of the project in November.

Officials at Gateway say they’ve already grown their staff of eight to 44 and taken other steps to respond to the audit’s findings.

Construction started on the tunnels earlier this year after federal officials, including U.S. Sen. Chuck Schumer, scored $11 billion in funding for the project. The rest of the price tag will be split between Albany and Trenton.

The tortured history of the Gateway Project could fill a book.

Then-Gov. Cuomo toured the existing and badly corroded Hudson River tunnels in 2018 as he attempted to push the Trump administration to approve the Gateway project.

Officials on both sides of the Hudson River have campaigned for new tunnels under the river for decades to relieve overcrowded trains, which were frequently delayed by breakdowns that would cascade because of schedules that had no slack.

All the while, traffic at the tunnels and George Washington Bridge continued to worsen.

The first major attempt, dubbed ARC, was controversially cancelled by then-New Jersey Gov. Chris Christie in 2010, who cited concerns about cost overruns and then diverted funds to pay for road repairs.

The existing tunnels were then badly damaged when they were flooded by salt water by Superstorm Sandy.

This 2015 image of the tunnels captures their deteriorated state following the Superstorm Sandy. The salt water played havoc on the wiring, leading to massive service disruptions that reignited support for the Gateway project.

ARC’s successor, Gateway, was delayed for years over struggles to obtain funding and — New York and New Jersey officials alleged — by President Trump’s administration in its feud with the two heavily Democratic states.

The tunnels will provide a critical second route between New Jersey and Penn Station, where a train breakdown or wiring problem can cause massive delays that ripple across the whole East Coast.

They will also allow the railroads to potentially double the number of trains that can run between New York and New Jersey — provided either substantial upgrades are made to the existing Penn Station hub or the railroads move ahead with controversial plans to build a potentially $17 billion station expansion.

A Gateway spokesman disputed the federal findings.

“We’ve been working hand in hand with the FTA on a refreshed, more advanced and accurate estimate that we anticipate finalizing in the coming weeks,” said spokesman Stephen Sigmund.