Kamran Faisal, an Assistant Director of the National Accountability Bureau, was found hanging from a fan in his room at the Federal Lodges in Islamabad, police officials said.
Preliminary investigations suggested he had allegedly committed suicide, they said.
Islamabad Police chief Bin Yamin told reporters the cause of death would be established by an autopsy.
Doctors who performed the autopsy at state-run Pakistan Institute of Medical Sciences refused to talk to the media about their findings.
Interior Minister Rehman Malik said he had ordered a magisterial inquiry into the incident.
A six-member medical board was formed to help determine the cause of death.
Several of Faisal's relatives at his hometown of Mian Channu in Punjab province alleged that he could have been murdered for his role in investigating accusations that Prime Minister Ashraf had taken bribes from companies that set up "rental power plants".
They asked the Chief Justice of the Supreme Court to order an independent investigation.
Faisal's father Abdul Hamid told reporters that his son rarely spoke about his work.
His uncle Tariq Masood said he had last spoken to Faisal on phone at 9 pm last night.
"He was normal and under no mental pressure. He was happy and doing his work diligently," Masood said.
Mohammad Afzal, a cousin of the dead official, said
Faisal may have been facing "pressure and worries" because of the important case he was handling.
"He could not have committed suicide. He must have been facing problems or someone misbehaved with him. We ask the Chief Justice to order a transparent inquiry," he said.
Faisal was one of two investigation officers probing allegations of graft in the rental power projects.
The allegations against Ashraf date back to his tenure as Power Minister.
The Supreme Court had directed NAB in March last year to take action against Ashraf and over 20 other suspects in connection with the allegations.
On Wednesday, the apex court directed NAB to arrest Ashraf and the other suspects.
NAB chief Fasih Bokhari told the court yesterday that he lacked evidence to make arrests.
Bokhari said investigators had not uncovered enough evidence against any of the suspects.
Faisal and the other investigation officer were recently suspended after they submitted a report on their probe to superiors.
Geo News channel quoted its sources in NAB as saying that Faisal had been "under pressure".
The Express Tribune website said "more than 20" unnamed NAB officials had alleged Faisal's death "was murder which was being framed as suicide".
Faisal had written to his superior last November, asking to be taken off the investigation into the power projects as he was not equipped to handle such a "mega case".
He wrote in the letter that he had only handled minor cases related to illegal assets and illegal appointments while serving in NAB.
Former colleagues told the media that Faisal had been under increased pressure after the apex court recently resumed hearing the case against the premier.
The "rental power projects" scheme was launched by the government in 2009 to address Pakistan's growing energy needs.
Islamabad: A senior Pakistani investigator probing graft charges involving Premier Raja Pervez Ashraf was found dead in mysterious circumstances at his official accommodation here on Friday, with his relatives alleging that he may have been murdered.
First Published: Friday, January 18, 2013, 14:18