More than 200 houses were demolished at Senti Kumi village in Likoni on Saturday.
Last year, the Government announced plans to demolish houses it said were standing on the path of ships calling at the port of Mombasa.
The demolition team arrived at 6am.
Ms Brenda Ombati, a mother of two, fainted when a bulldozer from the National Youth Service approached her house, prompting Land Commission (NLC) chairman Muhammad Swazuri to suspend the demolitions and give the house owners up to Friday to clear their structures.
“We do not intend to hurt anyone. This a Government directive to clear the route for ships calling at our port to avoid an international ban,” said Prof Swazuri.
He explained that the villagers had been served with a notice to vacate the shipping route in January last year but did not comply.
He said the Kenya Maritime Authority wrote to NLC in 2014, seeking to have those who had encroached on the shipping route removed after the International Maritime Organisation threatened to stop ships from sailing to Mombasa until their routes were cleared.
Swazuri was accompanied by Likoni Deputy County Commissioner Eric Wamulevu, OCPD Benjamin Rotich and at least 20 armed police officers.
Tenants claimed they had lost property worth millions of shillings and denied receiving an eviction notice.
One of them, Ali Ibrahim, said he had lost more than Sh5 million after his storey building was pulled down.
“It is not true that we were served with a notice to vacate last year. The Government should compensate us,” he said.
Mr Wamulevu said the demolitions would resume after Friday and warned the people to move out.
He said surveyors marked the buildings to be brought down.
Swazuri said a multi-agency team was marking out all the 21 fish-boat landing sites at the Coast in accordance with a directive by President Uhuru Kenyatta to have them repossessed.