Security agencies in Lamu, Tana River and Garissa counties have begun implementing the dawn-to-dusk curfew imposed by on Saturday.
In Lamu, the curfew imposed by acting Interior Cabinet Secretary Fred Matiang’i is being implemented by the multi-agency team in charge of Operation Linda Boni.
The operation involving the Kenya Defence Forces, the National Police Service, the National Intelligence Service (NIS) and other State security agencies is aimed at flushing Al-Shabaab out of Boni Forest.
On Sunday night, people's movements were restricted in the targeted areas of Halugho border, Galmagala, Sangailu, Masalani, Bodhei, Milimani, Baure, Basuba.
Villagers also stayed indoors in Mangai, Maralani, Ijara, Hola, Garsen, Kipini, Kiunga and Ishakani.
Lamu Island, Manda and Pate were excluded from the curfew.
Operation Linda Boni director James Ole Serian on Monday urged residents to cooperate with security officers enforcing the curfew.
“We are focused on ensuring there is security in our area,” he told the Nation.
In a Kenya Gazette notice dated July 8, Dr Matiang'i said the curfew would remain in force for three months.
It is not the first time a curfew is being imposed on Lamu.
On June 20, 2014, the government imposed a one-month curfew in the wake of the Mpeketoni terror attack that left dozens dead.
The initial period was subsequently extended by five months, prompting the Law Society of Kenya to file a case against the Inspector-General of police, the Attorney-General, the Interior CS and the Defence CS.
In April 2015, High Court Judge Said Chitembwe lifted the dusk-to-dawn curfew imposed on the mainland areas that include Mpeketoni, Hindi and Witu.
The court agreed with the LSK that the extended restriction on movement was "well outside the period provided for under the law”.
Implementation of the new curfew came as more troops were deployed to pursue Al-Shabaab militants in Boni Forest.
A source said Kenya Defence Forces soldiers on Sunday night bombed part of the Boni Forest to flush out the attackers believed to be hiding there.
"The operation to flush persons who attacked Pandaguo is going on well,” he said.
“We have deployed more troops and are aggressively pursuing the attackers. Very soon we shall get them.”
He clarified that the government was not behind the evacuation of residents of Jima and other operation areas.
"We are appealing to the media and the general public to avoid spreading alarming information about the operation,” he said.
“We are not aware of any missing persons in the operation area," he said.
Kenya Red Cross Society personnel on Saturday started helping to evacuate non-locals living in Jima to safety over fears of fresh Al-Shabaab attacks after the militants killed nine people on Friday night.
About 15 heavily armed Al-Shabaab terrorists are said to have rounded up the residents before targeting only men and beheading them with knives.
They killed at least nine people during the attack, just two kilometres from the Pandaguo police post, where they killed four police officers on Wednesday.