Five days after he published an account of abduction and torture by suspected Pakistani intelligence agents, a journalist working for the Guardian has been badly beaten by uniformed men who said they wished to "make an example" of him.

The assault revived concerns about media freedom in Pakistan, one of the world's most dangerous countries for journalists. Three weeks ago, another reporter, Saleem Shahzad, was beaten to death after disappearing from the capital.

Men wearing police uniforms stopped Waqar Kiani, a 32-year-old local journalist who has worked for the Guardian, as he drove through Islamabad on Saturday night, and ordered him to get out of his car. As he stepped out, four men landed a flurry of blows with fists, wooden batons and a rubber whip. Two others watched from inside the jeep. "They said 'You want to be a hero? We'll make you a hero'," said Kiani, who was recovering from his injuries . "Then they said: 'We're going to make an example of you'."

It was the second time Kiani had been targeted. Last Monday the Guardian revealed he had been abducted from central Islamabad in July 2008, blindfolded and taken to a safe house where interrogators beat him viciously and burned him with cigarettes.

The ordeal ended 15 hours later when his abductors dumped him 120 miles from Islamabad, warning they would rape his wife "and post the video on YouTube" if he told anyone.

Kiani had been working on a story about the illegal detention and torture of Islamist militants by Pakistani intelligence in collaboration with MI5. His research led him to an office of the Intelligence Bureau, the main civilian spy agency.

Although his abductors did not identify themselves they displayed detailed knowledge of Kiani's bank account, movements and contacts with Guardian journalists, leading him to conclude they worked for the government.The Guardian withheld Kiani's story for three years until last Monday. Kiani later gave a detailed interview about his experience to a local television channel. He believes the coverage triggered Saturday's vicious assault, which occurred after he went out to buy milk. "There is zero tolerance among our government and military establishment," he said. "They don't want us to speak the truth."

The Pakistan Federal Union of Journalists condemned the attack, demanding the government ensure security for journalists "at all costs". Interior minister Rehman Malik ordered a judicial inquiry by a magistrate and a police inquiry. "I have acted without any delay. The investigation is on, without any issue," he said.

The assault comes amid an unprecedented anger over the behaviour of Pakistan's intelligence and security forces. There was widespread shock earlier this month at video footage of paramilitary soldiers shooting an unarmed 22-year-old man in a Karachi park, then leaving him to bleed to death. Six soldiers and one civilian face murder charges. A similar shooting of five unarmed Chechens, one a pregnant woman, in Quetta last month is also under investigation.

The normally voluble media has been shaken by the discovery of the battered body of Shahzad, a specialist in Islamist militancy and the secretive military, in a canal in Punjab three weeks ago. Human Rights Watch said it had credible proof that Shahzad had been abducted by Inter-Services Intelligence, the military's top spy agency. The army strenuously denied involvement, describing the claims as "unfounded and baseless".

A government investigation into his death has become mired in controversy after a judge nominated to head the probe said he would not participate.

With 16 journalists killed in the past 18 months, Pakistan is the world's most dangerous country for journalists. Reporters die in suicide bombs, political violence and assassination, targeted by both Islamist militants and government agents.

Kiani was discharged from hospital on Saturday night after being treated for injuries to his chest and back. Guardian editor Alan Rusbridger said he was "extremely disturbed" to hear of his maltreatment.

"We call on the Pakistani authorities to investigate this latest beating and to give Mr Kiani meaningful protection against further attacks," he said.

Kiani said he had no regrets about going public with his account of torture. "I don't feel I did anything wrong. Journalists can't be silent forever in Pakistan," he said. "If we don't bring up the facts, then it's no longer journalism – we become spokesmen of the government."