Pakistan's army demanded the closure of the country's most popular television channel on Tuesday following allegations that the military's main intelligence agency had ordered an assassination attempt on its star journalist.

In a three-page petition to Pakistan's broadcast regulator the ministry of defence accused Geo News of mounting a "vicious campaign" to libel the Inter-Services Intelligence Directorate (ISI) and called for its operating license to be revoked. "The telecast in question was aimed at undermining the integrity and tarnishing the image of state institution and its officers and falsely linking it with terrorist outfits," the notice said.

The confrontation between the country's most powerful institution and its biggest media group was triggered on Saturday when Hamid Mir, a household-name presenter, was severely injured when gunmen opened fire on his vehicle as he was travelling along one of Karachi's busiest thoroughfares.

Even as he underwent emergency surgery Geo News broadcast non-stop claims, relayed by Mir's brother, that the ISI and its director general Zaheer-ul-Islam should be held responsible for the attempt to kill him.

Mir said he had feared he would be targeted because of his criticism of the army over its interference in politics and the brutal counterinsurgency being waged in the troubled province of Balochistan.

Outspoken journalists run great risks in Pakistan, particularly from militants who have targeted media workers who dare to criticise the Taliban or highlight deadly sectarian attacks on religious minorities.

Raza Rumi, a prominent liberal analyst, fled the country after he survived a gun attack on his car in Lahore that killed his driver in late March.

Recently Mir had demanded the high treason trial of former military ruler Pervez Musharraf be expanded to include other people involved in ordering emergency rule in 2007. The trial, which has dragged on since December, has become an area of tense disagreement between the government which initiated it and the military which wants Musharraf to be allowed to leave the country.

In a public show of support on Monday Nawaz Sharif, the prime minister, visited Mir in hospital and promised a thorough investigation into the assassination attempt.

The ISI has a reputation for being an all-powerful "state within a state" and has in the past been accused of various misdeeds, including the killing of journalist Saleem Shahzad in 2011 who had been investigating the penetration of al-Qaida into the army.

But never before have such serious claims of criminality been made by a such a prominent figure as Mir, a widely admired journalist whose night time show attracts front rank politicians as guests and is watched by millions. Although Geo later insisted it respected the military and had reported the army's denials alongside Mir's claims, the affair has caused uproar within army ranks.

Any move to put out of business the most prominent of all the private channels will be met with alarm by supporters of greater democracy in the country.

The Committee to Protect Journalists (CPJ) said Pakistan's broadcasting regulator should not act on the "spurious complaint" and called on the country's security services "to recognise the critical role of the media and exercise tolerance and maturity".

"The ISI is free to rebut allegations in the media but should not try to censor coverage," said Bob Dietz, the CPJ's Asia programme coordinator.

The immense power of Pakistan's army, which has directly ruled the country for half of its history, has been increasingly challenged since 2007 by the return of civilian governments and the dramatic rise of a rambunctious television news media.