There has been an increase in violence against journalists in Pakistan, a US rights group says.
General Musharraf - came to power as head of the army
The New York-based Human Rights Watch says press freedoms have eroded ever since General Pervez Musharraf came to power four years ago.
In an open letter to the president, the organisation said journalists were systematically threatened, tortured and detained without charges.
It highlighted the cases of two journalists who were allegedly threatened and tortured by the Pakistani security forces.
Amir Mir, senior assistant editor of the monthly magazine Herald, was allegedly criticised by the president last month at a reception for Pakistani newspaper editors, the rights group said in a statement.
President Musharraf is reported to have condemned the Herald as being anti-army in comments published in Mr Mir's stories.
"Two days later, unidentified persons set Amir Mir's car ablaze outside his house," the rights group said, adding that Mr Mir then received a message warning that this was just the beginning.
Human Rights Watch also highlighted the case of Rasheed Azam, a journalist from the province of Balochistan, who was arrested on charges of sedition in 2002.
The organisation alleges it has learnt that Mr Azam was tortured and abused during his detention by the military.
"General Musharraf should publicly disassociate himself from the comments about the Herald and order an investigation into the attack on Amir Mir's car," said Brad Adams, executive director of the group's Asia Division.
It was time for the president to show the world whether he was a reformer, or no different from other military rulers, Mr Adams added.
Information Minister Sheikh Rashid Ahmed denied journalists were being harassed, saying Pakistan's press freedoms were unmatched in the region.
"They can write whatever they want to write and
stories in the Herald are a proof of that," he told Reuters news agency.