The office of Prime Minister Nawaz Sharif has repeatedly rejected the article as inaccurate and the journalist who wrote it was at one point temporarily barred from leaving the country.
The military on Friday said top PML-N leaders - including finance minister, interior minister, and Sharif's brother - met the army chief Raheel Sharif, who is not related to the prime minister, to discuss the Dawn leak.
The development comes after the October 7 Dawn story "Act against militants or face worldwide isolation, civilians tell military", which forced the government to initiate an inquiry to identify the person responsible for its leak, Dawn reported.
A statement from Pakistani Prime Minister Nawaz Sharif's office had said the controversial story was a breach to national security and evidence so far collected links Rashid responsible for the lapse..
Speaking to DawnNews, PM spokesperson Musadiq Malik said, "A committee has been formed for investigation of the Dawn story which is in the final phase of its probe".
Federal Information and Broadcasting Minister Parvez Rasheed has been removed from his post on Saturday, TheNewsTribe.com reported. "The investigation is being done with all sobriety, all responsible will be punished".
"An including committee including senior officers of ISI, IB and MI is being formed by the Government to Pakistan to clearly apportion blame, identify arrests and motives and expose all those responsible for this episode of stern action in the national interest", it said. The meeting was also attended by Director General ISI General Rizwan Akhtar.
On Saturday, the prime minister's office said the October 6 story was "planted" and termed it a "breach of national security".
The widely read daily stood by the story issued on October 6, saying it was "verified, cross-checked and fact-checked".
Almeida's name was put on the Exit Control List but the ban was later lifted after the backlash against the government.
Pakistan army had dismissed the story as "unfounded" and called for a probe into the security meeting's leak. Instead he said the government will be responsible.