Pakistani police also arrested the head of Axact in the early hours of Wednesday following a raid on the company's diploma printing operations, and registered a criminal case against him, investigators said.
The interior ministry wrote to the Federal Bureau of Investigation (FBI) on Tuesday seeking assistance.
Officials said a letter had been sent to the US State Department.
The request came days after a New York Times article said that Axact had run a global network of fake online universities that manipulated customers and generated tens of millions of dollars in estimated revenue annually by selling bogus diplomas.
Axact has denied the allegations, calling them "baseless".
A senior interior ministry official, who did not wish to be named, said: "This is a scam whose victims are mostly people outside of Pakistan, in the US, UK and the Middle East.
"It was inevitable for the FBI to get involved in a scam in which so many Americans have allegedly been cheated. We will also reach out to Interpol in the coming days."
The allegations, which have dominated Pakistani headlines in recent days, are an embarrassment for a government already under pressure from a faltering economy, with people questioning why regulators appeared to be wrong footed.
Officials from Pakistan's Federal Investigation Agency (FIA) questioned Axact's CEO Shoaib Shaikh for several hours on Tuesday night in the southern port city of Karachi, where the company is based.