The New Age reported that Karegeya, 53, had been living in exile in South Africa for a number of years. He was found dead in the Michelangelo Towers Hotel in Sandton, Johannesburg, last Wednesday.
Private investigator Chad Thomas told the paper that Rwanda's Lt-Col Francis Gakwere was among those arrested in Maputo, Mozambique, for Karegeya's murder.
"Gwakere was also a prime suspect in the failed hit on General Kayumba Nyamwasa in 2010 but there was insufficient evidence to allow the charges to stick," Thomas was quoted as saying.
Three other suspects were still on the run.
Karegeya's nephew David Batenga said he last saw his uncle with a close family friend Apollo Kiririsi at the hotel.
The New Age reported that Kiririsi had since been seen in Rwanda and had denied any involvement in the killing.
Former Rwandan army chief-of-staff Lt-Gen Kayumba Nyamwasa and others have accused Rwandan President Paul Kagame of ordering Karegeya's assassination.
Kagame has denied the claims.