The report, written by journalist Cyril Almeida for the 'The Daily Dawn' -- one of Pakistan's leading English language papers -- on October 6, said the civilian government had clashed with military chiefs
over the issue of homegrown militancy in Pakistan.
Almeida, who was attempting to fly out on a holiday on Monday evening was informed that he had been placed on the Pakistan's Exit Control List, which prevented him from leaving the country.
The Exit Control List is a border control system that is maintained under ordinance by the government of Pakistan. It allows the government to ban people whose names appear on the system from exiting Pakistan.
Almeida tweeted that he had been placed on the list Monday night, causing a social media storm with journalist, analysts and supporters tweeting under the hashtag #StandWithCyril.
'Verified, cross-checked and fact-checked'
Almeida's column was published amid a backdrop of increasing tensions between Pakistan and India over Kashmir
. It highlights tensions between senior members of Pakistan's civilian government and the director of ISI, the country's military intelligence organization.
The Pakistani government responded swiftly to Almeida's column, dismissing it as "an amalgamation of fiction and fabrication" in a statement.
The Daily Dawn's editor Zafar Abbas issued a statement Tuesday, asserting that Almeida's column was "verified, cross checked and fact checked."
He also said the government should refrain from "targeting the messenger and scapegoating the country's most respected newspaper in a malicious campaign."
'Stern action' called for 'speculative reporting'
In a statement released Monday, the Pakistani prime minister's office stated that a high level meeting on the report had taken place between the prime minister, the chief army staff, interior minister and the director general of the ISI, with calls for "stern action" against "those responsible for speculative reporting."
Yet the public response to the story has caused some to question if Prime Minister Nawaz Sharif's democratically-elected government is losing support in Pakistan.
Analyst and author of Military Inc, Ayesha Siddiqa, told CNN that Almeida's placement on the Exit Control List is "against the norms of democracy."
Amnesty International called the travel ban on Almeida "a crude intimidation tactic designed to silence journalists and stop them from doing their jobs," in a statement released Tuesday.
Columnist Mosharraf Zaidi told CNN that Almeida's report had confirmed what was already widely known in Pakistan. He asserted, however, that the significance of Almeida's report lay in how forcefully he had "disrupted the national conversation" by placing the issue of tensions between civilian government and military into the public arena.