The NASA strategist was arrested at night and his whereabouts remain unknown.
According to Raila Odinga's spokesman and private secretary, Dennis Onyango, Ndii was arrested because of his appointment to lead the people's assembly.
"One Mr Aleng Peter Gimwani, Service. No 234336 from the Flying Squad and five officers picked Dr David Ndii a few minutes ago from Leopard Beach Hotel in Kwale.
"Alenga told Ndii's wife that they are taking him to Diani Police Station. But Ndii is not at Diani. They have taken him somewhere else known only to Mr Alenga," Onyango tweeted.
Siaya Senator James Orengo claimed that Ndii was not at Diani police station as claimed by the police.
Last week Ndii was picked by NASA alongside seven other members to guide the coalition on the way forward of the People's Assembly.
The members include Senator Judy Sijeny, Oduor Ong'wen, Dr Mutakha Kangu, Peter Mathuki, Hamida Kibwana and Koitamet Olekina.
The committee will be responsible for coordinating programmes of all county assemblies that have passed the motion for the formation of the people's assembly.
By the time of publishing the story, it was still not clear where the NASA strategist was being held by detectives.