Human Rights Watch (HRW) sent a letter to Pakistan President Pervez Musharraf on Tuesday concerning the case of one journalist.
Musharraf, a US ally in the "war on terror," seized power in a 1999 military coup.
"In the letter, Human Rights Watch highlighted the case of Amir Mir, senior assistant editor of the monthly magazine Herald, whom Musharraf reportedly threatened at a 20 November reception for Pakistani newspaper editors," the rights group said in a statement.
In comments directed at Mir's stories, Musharraf reportedly condemned the Herald for being anti-army and working against the "national interest".
"Two days later, unidentified persons set Amir Mir's car ablaze outside his house," the rights group claimed, adding Mir then received a message purportedly from Pakistan's intelligence services warning that this was "just the beginning."
"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 HRW's Asia Division.
"It is time for General Musharraf to show the world whether he is a reformer - or no different from other military rulers," Adams stressed.
HRW also raised the case of Rasheed Azam, a journalist and political activist from Khuzdar in Balochistan province, who was arrested on sedition charges in 2002. HRW says it has learned that Azam was tortured and abused during his detention by the Pakistani army.
The rights group added that many Pakistani reporters had been detained without charge, mistreated, tortured, and otherwise denied basic legal rights.
"While your government has consistently claimed that the press in Pakistan enjoys 'unprecedented' freedom, independent monitoring groups such as Reporters Sans Frontières (RSF) have documented the steady erosion of press freedom under your government", the letter stated.
In October 2002, Pakistan was ranked at 119 out of 166 countries in the RSF Press Freedom Index. By October 2003, this ranking had slipped to 128.