Interior Cabinet Secretary Fred Matiang'i has blamed the resurgence of Al-Shabaab attacks in north-eastern and Coast regions on collaboration of terrorists with local communities.
Dr Matiang'i announced that security officers will launch an operation to deal with the menace.
He said officers will not distinguish between terrorists and those who harbour them.
"We must decimate terrorism, and this is through taking the war to the next level by making it painful. The major challenge that we face is the level of collaboration and collusion of local communities with terror groups. We are going to deal with them," said Dr Matiang'i.
The CS said the recent attacks in Wajir, Garissa and Lamu counties were a result of locals harbouring criminals and failing to share information with the authorities. "The government will not distinguish between terrorists and those who harbour them because they are also criminals, and we will deal with them as such," said Dr Matiang'i.
"It is not right for citizens to give terror groups accommodation for whatever reason," added the CS.
Dr Matiang'i said chiefs and their assistants will profile families who have been hosting the terrorists.
"The government will invest more resources to strengthen its capacity and capability to fight terrorism. We must face this menace. We will not be intimidated or bow to pressure from politicians or any other person," he said.
Dr Matiang'i's announcement follows an increase in attacks by Al-Shabaab insurgents, which have recently claimed 21 lives, including American soldiers, pupils and teachers. North-eastern and Coast regions have been the most affected. The insecurity has seen some teachers and residents flee the affected areas.
The latest attack was at Kamuthe Boarding Primary School in Dadaab, Garissa County, where three teachers were killed. This came a few days after another attack at Saretho Boarding Primary School in the same county, where four pupils were killed.
The two attacks came in the wake of a raid by an al-Qaeda-affiliated group on Manda-Magogoni military base in Lamu, where three United States service members were killed.
The attack raised security concerns in the tourism-rich county, which has suffered massive losses in previous terrorist raids.
Sources blamed the attacks on local terror cells. "They have been active. These people were waiting for the right time to strike, many alerts were issued by the government last year," said the source.
The source said new recruits were being used to carry out attacks.
Lamu County Commissioner Irungu Macharia acknowledged reports that youths from the Coast were among those being recruited to join Al-Shabaab.
"These youths are the ones being used to conduct these heinous attacks on our people. But be assured that we will deal with them. They should rest assured that they are going to be dealt with," said Mr Macharia.