The body of Kamran Faisal was found hanging from a ceiling fan in his room at a government dorm in Islamabad, according to senior police officer Bani Yamin.
"Apparently it seems he committed suicide, but we are sending his body for autopsy to determine the cause of death," Yamin said.
Faisal's death came days after the Supreme Court ordered the arrest of Prime Minister Raja Pervaiz Ashraf and 15 others in connection with an old corruption case that the officer was investigating.
The prime minister was implicated in the case when he was minister of water and power. At the time, he oversaw the import of short-term power stations that cost the government millions of dollars but produced little energy.
Ashraf has denied the charges against him.
Faisal and another investigating officer of the National Accountability Bureau, Asghar Ali, played a main role in the graft probe until they were removed from the investigation weeks ago by Fasih Bokhari, the bureau chairman who was allegedly unhappy with their performance.
Pakistan's Supreme Court on Tuesday asked the NAB to arrest Ashraf and 15 others involved in the case. But Bokhari, refused, saying he does not have sufficient evidence to arrest the prime minister.
The refusal was seen as the latest clash between the government and the country's top court and has intensified the sense of political crisis in Pakistan.
Bokhari said he needed more time to determine whether the premier should be arrested. The top court on Thursday adjourned the hearing in the case for next Wednesday.