Bodies identified as those of missing lawyer Willie Kimani and taxi driver Joseph Muiruri were on Friday found in a river in Ol-Donyo Sabuk, Machakos County.
The two bodies have been transferred to City Mortuary in Nairobi.
A third body, thought to be that of Mr Kimani’s client Josphat Mwenda, slipped back into the river.
Directorate of Criminal Investigations boss Ndegwa Muhoro said efforts to retrieve the missing body are under way.
At City Mortuary, the superintendent in charge said two bodies were brought in by police at 8.15am from Ol-Donyo Sabuk.
Some of the mortuary attendants said the bodies were found with their hands tied behind their backs.
The records at the morgue show that the cause of their deaths was drowning.
Law Society of Kenya advocate Dan Kinuthia said the two were severely beaten and strangled. Their bodies are swollen and in bad shape, he said.
He said he identified the lawyer, "because he was my friend. He was a tiny guy but his body is too swollen ... likely they killed him a long time ago," he said outside the mortuary.
The second body, Mr Kinuthia said, was beaten up, had an ear missing and the hands were tied with a sisal rope.
Earlier on Friday, a court had given Police Inspector-General Joseph Boinnet and the Directorate of Criminal Investigations up to 2pm to issue an interim report on the status of investigations over the disappearance of the three people.
The three were suspected to have been abducted by Administration Police (AP) officers on June 23.
The court heard that the missing were last seen entering the Syokimau AP camp in Machakos County before they disappeared.
During the hearing, lawyers wanted the government to be compelled to disclose their whereabouts.
They told the trial court that it is the responsibility of the State and representative agencies to ensure the safety of its citizens.
(Additional reporting by Vincent Agoya; editing by Basillioh Mutahi)