Nyang’aya was shot when six armed thugs raided his houses at about 11pm, police said.
“He sustained two gunshot injuries but he is out of danger,” a senior police officer briefed on the matter said.
The renowned human rights defender was admitted to the Karen Hospital.
Police said they were investigating the incident in which the Amnesty boss also lost money and other valuables.
“We have not established the motive of the attack. The matter is still under investigation and no suspect has been arrested,” the officer said.
Armed crime has been on the rise in recent weeks running into the festive season, despite assurances from the police that adequate security measures are in place.
Interior Cabinet Secretary Joseph ole Lenku said more officers will be deployed to various parts of the city for enhanced patrols.
“We are doing everything within our means to ensure the country is safe, we are appealing for more public participation to fight crime,” Lenku said.