A prominent Pakistani journalist who was banned from leaving the country after infuriating the army with a front page scoop about its clandestine support of jihadi groups has been removed from the “exit control list”.

The interior minister, Chaudhry Nisar Ali Khan, said he had agreed to remove the name of Cyril Almeida, a columnist and reporter for the Dawn newspaper, from the travel ban list as a “goodwill gesture” following a meeting with media representatives.

In a statement on Friday, the interior ministry said an ongoing leak inquiry would “continue to its logical conclusion”.

The inquiry is taking place amid renewed tensions between Pakistan’s civilian and military rulers.

The government had endured days of criticism by the media and human rights groups after Almeida was told he would not be permitted to go on a long-planned family holiday to Dubai on Tuesday.

The travel ban followed his report of a highly unusual rebuke by Pakistan’s government of the country’s military for supporting jihadi groups.

According to Dawn, senior generals were told at a closed-door meeting that the continued presence of militant groups who fight in India and Afghanistan but operate from Pakistan had made the country isolated internationally.

Rizwan Akhtar, the director general of the Inter-Services Intelligence directorate (ISI), a military spy agency, was told the army must not block action against Jaish-e-Mohammad, Lashkar-e-Taiba and the Haqqani network, three groups that have remained untouched despite Pakistan’s much-vaunted campaign against terrorism in the last two years.

The story was officially denied by both the government and the army.

Military sources say they are not angry with Almeida for what one described as a “professionally well-executed story” but for what they are convinced was a government official for leaking details of the meeting.

One security official said it was part of a campaign by the ruling faction of the Pakistan Muslim League led by the prime minister, Nawaz Sharif, to deliberately “malign the army and ISI”.

Military fury was underlined on Friday at a meeting of the army high command.

A statement about the gathering of corps commanders said: “Participants expressed their serious concern over feeding of false and fabricated story of an important security meeting held at PM house and viewed it as breach of national security.”

Sharif’s three years in power have been punctuated by explosive rows with the military, which has directly ruled Pakistan for more than half of its history and is still thought to control defence and foreign policy.

The first standoff came when the prime minister ordered a high treason trial of Pervez Musharraf, the former army chief who deposed Sharif in a 1999 coup.

Sharif’s party was later caught up in a confrontation between the army and a broadly pro-government media group that accused the ISI of attempting to assassinate its most famous journalist.

Analysts say the prime minister currently enjoys a somewhat stronger hand in the run-up to the retirement of the army chief next month and the selection of his successor, one of the few powers Sharif has over the army.