One of the bodies was found dumped in a thicket while the other was traced to a mortuary in the town.
The two are Mombasa-based Muslim cleric Samir Hussein who was facing a terror-related charge while the other is Muhammed Kassim, a blind man who had been arrested and released by police in Nairobi last month.
Both bodies were badly mutilated and had eyes gouged out.
The body of Hussein was discovered in a thicket in Voi late on Thursday while that of Kassim was found at the Wundanyi hospital mortuary on Friday morning.
Circumstances of their deaths remain unclear.
Hussein had been in and out of police custody over terrorism-related charges and had a case that was due for mention at the Kibera Law courts on May 29, according to his lawyer Chacha Mwita.
“They were arrested four days ago (Tuesday) at the South Coast in the company of the blind guy. They have been missing until when their bodies were found,” Mwita said. He said there were other people missing but he did not give their details.
Police however, denied any of the two had been arrested as alleged and blamed the deaths on possible internal wars between members of the Al Shabaab terror group.
“None of those people were in our custody, we have checked all our records and none of them had been arrested lately,” Police Spokesman Eric Kiraithe said.
Kiraithe said an investigation had been launched to establish circumstances under which the two people were killed.
“Investigations are launched on any death, these ones will also be investigated, but we suspect it has to do with internal wrangles within the terror group,” Kiraithe said.
Reports indicate that Hussein, one of the two men found dead in Mombasa had fallen out with his associates in Mombasa, including a renowned cleric who is linked to terrorism activities and had once differed publicly during a court case.
The blind man whose body was found in a mortuary on Friday had been arrested and interrogated by police in Nairobi over the Machakos bus station blast before he was set free.