ISLAMABAD, Pakistan — A well-known Pakistani journalist has been found dead after being abducted over the weekend in an upscale neighborhood here and receiving repeated threats from Pakistan’s premier intelligence agency.

The journalist, Syed Saleem Shahzad, 41, wrote predominantly about security and terrorism issues for the Hong Kong-based Asia Times Online and the Italian news agency Adnkronos International. He disappeared Sunday evening in the center of this capital just two days after writing an article suggesting that a militant attack on the navy’s main base in Karachi on May 22 was carried out because the navy was trying to crack down on cells from Al Qaeda that had infiltrated the force.

Pakistan’s armed forces, specifically the navy, have been highly embarrassed by the 16-hour battle that ensued at the base when six attackers climbed over a wall and blew up two American-made naval surveillance planes. Ten people were killed in the attack, and American and Chinese technicians working on the base only narrowly escaped injury as they were driven out through a hail of bullets.

A former navy commando, Kamran Malik, was arrested Friday, along with his brother, in a sweep by Pakistani intelligence agents in connection with the attack.