Karachi, Pakistan - Pakistan's military has rejected Prime Minister Nawaz Sharif's decision to fire a top foreign policy adviser over his alleged connections to an article published last year that suggested there was a rift between civilian and military leaders on how to tackle militancy.

Sharif fired adviser Tariq Fatemi and ordered action against senior bureaucrat Rao Tehsin Ali on Saturday, said a statement from his office, adding that he was acting on the recommendations of an inquiry commission that probed the leaks, which formed the basis of the original newspaper report.

That report, published in the Dawn newspaper in October last year, suggested the civilian government had criticised the military for protecting certain armed groups operating in Pakistan, and sought a free hand to go after them. The military, the report said, had agreed to allow such action to be taken.

READ MORE: Pakistan - Cyril Almeida of Dawn 'on Exit Control List'

The prime minister also referred the case of the journalist who wrote the story and editor of Dawn to the All Pakistan Newspapers Society, an industry body, "for necessary disciplinary action to be taken against them".

In a rare public contradiction of the civilian government's orders, top military spokesman Major-General Asif Ghafoor said the military "rejected" the prime minister's orders.

"Notification on Dawn Leak is incomplete and not in line with recommendations by the Inquiry Board. Notification is rejected," he said.

Notification on Dawn Leak is incomplete and not in line with recommendations by the Inquiry Board. Notification is rejected. — Maj Gen Asif Ghafoor (@OfficialDGISPR) April 29, 2017

According to Pakistan's constitution, the armed forces are under the command and control of the elected civilian government. The military's press wing did not respond when asked by Al Jazeera what its "rejection" of the prime minister's orders entailed.

Pakistan's powerful military has ruled over the country for roughly half of its 69 years since independence from the British, and maintains tight control over security and parts of foreign policy.

The inquiry commission formed to probe the leaks that were the basis of the original story included members of the military's intelligence agencies, as well as from civilian law enforcement and a retired judge.

Following the military's "rejection", Interior Minister Chaudhry Nisar Ali Khan addressed the media in Islamabad, saying further action on the issue was possible. He implied the prime minister's notification was "leaked" to the media before his ministry had a chance to act.

Al Jazeera received the prime minister's notification through the PM Office's official press release channel, through which all routine statements are sent to journalists.

National security 'rift'

In October, the prime minister also fired then-information minister Pervaiz Rashid in connection with the leak.

In an unprecedented move, Cyril Almeida, the reporter who broke the story, was barred from leaving the country shortly after the story's publication, which both the government and military had rejected as a "fabrication".

His report centred on a conversation that reportedly took place during a secret October 3 meeting of the country's national security leadership, including the prime minister and the head of the Inter Services Intelligence.

READ MORE: Pakistan: Cyril Almeida removed from exit control list

The conflict in the meeting, Almeida reported, centred on the approach towards armed groups such as Jaish-e-Muhammad and Lashkar-e-Taiba, which target Indian security forces in Kashmir and elsewhere.

Dawn, Pakistan's most widely read English language newspaper, stood by the story despite the government and military declaring it to be a fabrication.

While Saturday's notification from the PM's office did not recommend specific action against Almeida or Dawn editor Zaffar Abbas, it did ask the All Pakistan Newspapers Society to develop a "code of conduct for the print media, especially when dealing with issues relating to security of Pakistan, and to ensure that stories on issues of national importance and security are published by abiding to basic journalistic and editorial norms".

Follow Asad Hashim on Twitter: @AsadHashim