According to AFP, operating out of the city of Karachi with 2,000 employees, the company Axact ran a fake education empire that involved paid actors promoting fictitious universities and even fake State Department authentication certifications bearing the signature of John Kerry, the article said.
The report, which quoted former employees and analysed more than 370 websites of fake universities, accreditation bodies and other purported institutions, sparked a wave of criticism on social media even as the company denied wrongdoing.
A message on its website declared the story "baseless, substandard, maligning, defamatory, and based on false accusations" and added it would sue the New York Times.
On Twitter, however, some users were unconvinced. "I mean, how is #Axact exactly going to prove defamation? Are they going to build dozens of university campuses overnight?" tweeted user Kaalakawaaa.
The company has said it will launch a news channel named Bol this year, which has already lured many of Pakistan's top TV anchors and journalists with reportedly the highest salaries in the market.
According to the report, Axact created a series of fake websites involving "professors" and students who were in fact paid actors.
The article cited clients from the US, Britain and the United Arab Emirates who had paid sums ranging from thousands to hundreds of thousands of dollars for their degrees -- with some believing the universities were real and they would soon receive coursework.
Axact and its CEO, Shoaib Ahmad Shaikh, did not immediately respond to requests from AFP for comment.
In the statement on its website, Axact did not directly respond to the allegations but instead accused domestic media rivals of colluding with the New York Times to plant a slanderous story in order to harm its business interests.
According to an official in Pakistan's Federal Investigation Agency who did not wish to be named, the allegations raised by the newspaper would be a crime under Pakistan's Electronic Transaction Ordinance, punishable by seven years in prison.
The official added that the FIA was aware of the issue but had not launched an investigation because it had not received a formal complaint.