Gunmen believed to be Al-Shabaab militia raided a village in Kiunga, Lamu County and killed two people before escaping.
Witnesses and police said the victims were shot dead at close range in the attack in Mararani area on Wednesday dawn. A combined team of security agents was sent to the area to pursue the killers.
The victims were on foot in the area when they were attacked.
"A team of security agents was dispatched there to pursue the killers and they are yet to communicate," said an officer operating there.
The incident came three days after President Kenyatta had ordered an operation on the militants.
"We shall finish them. When we get them, we will not jail but bury them," he said of the terrorists who have turned Boni Forest into a playground, attacking and killing locals before retreating there.
Speaking in Mpeketoni, the president told those living in areas prone to the attacks to vacate and give way for ongoing operation there.
He also asked locals in Lamu County to cooperate with security officers and give information that will help get the attackers.
The attacks have affected tourism, local economy and movement. A number of schools have also closed down because of the incidents. Given elections are scheduled for next month, it is still unclear if the locals will be able to vote.
Electoral body has urged police to ensure there is voting on August 8. A dusk to dawn curfew has been imposed in the area as part of efforts to tame the attacks in vain.
The area has received a facelift by the government under Operation Linda Boni as part of efforts to ensure locals receive services.
The head of an operation aimed at wiping out the militia from Boni Forest in Lamu County has been moved in changes.
Mr James Ole Serian was moved to Harambee House, Nairobi for redeployment. Lamu County Commissioner Mr Joseph Kanyiri was ordered to take over the operation immediately.
Thousands of people had been uprooted from their homes while businesses, public transport and farming ground to a halt. The deadliest attack happened in Mpeketoni and Pandaguo in 2014 where more than 90 people were killed.
The operation is being carried out by the Kenya Defence Forces (KDF), the National Police Service, the National Intelligence Service (NIS) and other State security agencies.
Officials said it is three-pronged: As KDF soldiers engage the militants in direct combat that involves aerial bombardments and infantry soldiers combing every inch of the forest, NIS detectives infiltrate neighbouring villages to pick out those collaborating with the terrorists, while police officers arrest and interrogate suspects with the aim of charging them in court.
But the attacks have resumed in the last month killing more than 18 people.
On Monday night, gunshots were heard in the area when the militants attempted to attack a police camp hours after president Kenyatta had ordered their killing.
Up to 18 people have been killed in the area for the last two weeks.
The latest happened on Thursday when the militants killed a bodyguard to Public Works PS Mariam El Maawy, her nephew, driver and two other people in Milihoi area.
The militants had killed 13 people in Jima and Pandaguo areas a week earlier.
The area has seen new wave of attacks in the past months claiming more than ten lives.
On June 27, four pupils and four policemen were killed in an IED attack launched by the militants in Kiunga on a police vehicle.
Security agents were had been warned of Al-Shabaab attacks within Kiunga area, Milihoi, after roughly 100 of them were spotted by locals.