The resurrection of St. Nicholas Greek Orthodox Church, destroyed on 9/11, has turned into an $80 million boondoggle — and now the feds want to know where the money went.

The US Attorney’s Office in Manhattan is probing the project’s finances and those of the Greek Orthodox Archdiocese of America, according to The National Herald, a newspaper covering the Greek community.

The state Attorney General’s Office is also investigating, reported the paper, which said as much as $15 million has gone missing from the construction accounts for the half-built church, to be called the St. Nicholas Greek Orthodox Church and National Shrine.

The project is funded by tens of millions in private donations.

Meanwhile, the project’s price tag has soared from $30 million to $80 million. And work came to a standstill in December when the archdiocese was unable to pay the contractor. The shrine was supposed to be completed in 2016.

The domed structure — made of the same Greek marble mined to build the Parthenon — is to replace St. Nicholas Greek Orthodox Church, which stood on Cedar Street until the 2001 terror attacks.

After years of negotiations, the church struck a land-swap deal with the Port Authority to rebuild on Liberty Street.

The new shrine was designed by Spanish architect Santiago Calatrava. His Web site says the house of worship, which will emit a glow at night, will be the only religious structure at Ground Zero and “a spiritual beacon of hope and rebirth.”

But with the heralded design came runaway costs. When Calatrava created the nearby Oculus transit hub, that project’s price tag also soared — to $4 billion.

What was supposed to be the new face of the Greek Orthodox church in America turned into a national embarrassment.

“The church has zero capabilities to manage a project like the St. Nicholas Shrine,” said Dean Popps, a Virginia lawyer and former leader of a church reform movement. “Let’s just say these guys aren’t the same Greeks who built the Parthenon.”

Jerry Dimitriou, a former archdiocese executive director, warned church officials in a January letter that design changes would cost “millions of extra dollars.”

“Were you not told, before Mr. Calatrava was chosen, that if you choose him as the design architect, the budget would surely be at least double what was originally estimated?” he wrote.

The vast majority of the design and material changes were requested directly by the Archdiocese and not the design architect, according to source close to the design team.

As of December, the church had collected only $37 million of $49 million in pledged donations for the project.

The church is now facing the heat of federal and state probes.

Bishop Andonios Paropoulos, chancellor of the Manhattan-based archdiocese, sent an e-mail to employees last week ordering them to preserve all documents.

“Deletion of any documents . . . (e.g., fundraising) could be considered an obstruction of justice,” the e-mail warned.

The archdiocese said an internal review of the project’s finances found a breach that prompted it to alert the AG to “concerns” related to the organization’s “payroll and credit-card statements.”

The archdiocese denied $15 million was missing, but its treasurer said some $4.75 million deposited in unspecified accounts had been transferred out, likely to close the archdiocese’s $5 million deficit.

The Rev. Alexander Karloutsos, who headed the fund-raising, told The Post that the church was still evaluating how much money was improperly transferred.

The US attorney and AG declined to comment.