This comes weeks after the mysterious slaying triggered condemnations and calls for an independent probe.
Meanwhile, Islamabad police charged two Pakistani businessmen living in Kenya who had hosted Arshad Sharif with involvement in his killing.
The report however did not provide any evidence for its claims and there was no immediate comment from Kenya.
The 50-year-old Sharif was hiding in Kenya to avoid arrest at home on charges of maligning Pakistan’s national institutions a phrase used for critics of the powerful military, which has ruled Pakistan for half of its 75-year history.
He was killed on Oct. 23, when the car he was in sped up and drove through a checkpoint outside the Kenyan capital and police opened fire.
Nairobi police later expressed regret over the incident, saying it was a case of “mistaken identity” during a search for a similar car involved in a child abduction case.
News of the killing shook Pakistan and days later, thousands came out for Sharif’s funeral as the nation mourned.
The international media watchdog Reporters Without Borders, the military, Pakistani journalists and Sharif’s family demanded an independent probe.
The investigators’ 592-page report, seen by the Associated Press, said the Kenyan police issued contradictory statements following the killing.
As part of the probe, two Pakistani officials had travelled to Kenya where they met with police and Sharif’s hosts, brothers Kuram and Waqar Ahmed.
According to the report, Kuram told the investigators that he was in the car with Sharif at the time of the shooting, travelling home after dinner. They saw the roadblock, which Kuram believed to have been set up by robbers. As they sped through without stopping, he heard the fatal gunshots.
Kuram said he then called his brother, who advised him to keep driving until they reached the family’s farmhouse, several kilometres (miles) away.
Once at the house, the brothers found Sharif was already dead, Kuram was quoted as saying.
Sharif had stayed in the United Arab Emirates after leaving Pakistan in August and before travelling on to Kenya.
The report further suggested that the bullet that fatally wounded Sharif was fired from either inside the car or from close range. It again did not elaborate.