Accountability Bureau, was yesterday found hanging from a fan in his room at the Federal Lodges, a government hostel in Islamabad.
Faisal was part of the team investigating allegations that prime minister Raja Pervez Ashraf had accepted bribes to clear power projects.
Faisal's uncle Tariq Masood told reporters at Mian Channu in Punjab province that he had seen injuries on Faisal's arms, wrists and back while bathing his body ahead of the funeral.
"There are marks on the wrists as if he had been tied. There are marks on the back and below the neck. It looks as if his right arm was tightly held," Masood said.
One of Faisal's cousins too told reporters he had seen the bruises.
Geo News channels aired footage of what it said were marks of injuries on the body.
News channels reported Faisal's father Abdul Hamid had shown the marks to reporters and demanded a judicial inquiry into his son's death. Faisal's relatives said they did not believe he had committed suicide.
Media reports have said Faisal had been "under pressure" and had written to his superior last November, asking to be taken off the investigation into the power projects.
A preliminary autopsy report submitted to police concluded that Faisal had committed suicide, said Sahrif Astori, a spokesman for state-run Polyclinic Hospital.
"Since this was a high-profile case, we formed a five-member board of surgeons, physicians, pathologists and other experts," he said.
"Following the autopsy and examination, the board's interim report said this was case of suicide. There were no marks of injury or bruises on the body except the rope marks on the neck," Astori said.
Samples had been sent for forensic tests and a final autopsy report is expected to be compiled in about 10 days, he said.
Faisal's colleagues, who visited his family in Mian Channu to offer condolences, demanded that the Chief Justice of the Supreme Court should take suo moto notice of the death and order a judicial inquiry.
Describing Faisal as a diligent and professional officer, the colleagues said he was handling a very important case that was being closely watched by the people of Pakistan.
Ehtaram Dar, an Additional Director of NAB from Lahore, told reporters: "Either he was murdered or he committed suicide – in both cases this is not a natural death. The government should look into the circumstances".
Media reports said Faisal's body was found by his colleagues after they were alerted by his family when he failed to answer his mobile phone.
His body was hanging from a fan with a table underneath. The room was not disturbed, the reports said. Faisal was one of two investigation officers probing allegations of graft in "rental power projects" that were cleared when Raja Pervez Ashraf was the 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 later told the court 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.