Federal investigators and armed officers shut down the main office of Axact in Karachi, seized computers and files, and held at least 30 people for questioning, according to the Times.
The company - which describes itself as Pakistan's largest software exporter - came under fire on Sunday after the Times alleged it makes tens of millions of dollars a year by selling bogus high school, college, and doctoral degrees.
Axact reacted to Sunday's story in the Times with an excoriating post on its website, vehemently denying the claims, and calling it defamatory, baseless, and "merely a figment of imagination."
Though Axact has attempted to silence the media from reporting the allegations, it has been unable to stop Pakistan's main television stations, which have aired several negative stories about the company, following the Times' original story.
Axact's strategy is one of smoke and mirrors, according to the The Times. Its 370 websites include news reports that contain accolades about the strength of their program and feature fake actors who pose as college professors, The Times reports.
The Times article even includes a certificate with an apparently forged signature from Secretary of State John Kerry, which is just one of techniques Axact reportedly utilizes to provide credibility to the program. But the diplomas, which can cost about $350 for high school degrees, and $4,000 or more for doctoral degrees, are reportedly worthless upon closer inspection.
Following Sunday's article, Axact lashed out at the reporter of the story, Declan Walsh, calling it an "exemplary display of poor journalistic skills and yellow journalism." The company also implied that Walsh was not an objective person to write about Pakistan due to a prior instance where he was expelled from the country for supposedly damaging its national interests.
While Pakistan's Interior Ministry ordered the expulsion of Walsh in 2013, it offered only vague indication for the reason behind the decision.
"It is informed that your visa is hereby canceled in view of your undesirable activities," the order stated. "You are therefore advised to leave the country within 72 hours."
Advocates for free press were disturbed by the move and said that it reinforced the Pakistan's reputation as unwelcoming for journalists, according to a 2013 article in the Times.
We reached out to Axact to give it a chance to provide additional comment on the article. A spokesperson for the Times said, "We are confident in our reporting and see nothing in the response that would prompt a correction."