Kenyan security forces have destroyed five camps used by Al Shabaab in a sweep of Boni Forest, a commander in charge of the operation said.
The army and police launched the operation two months ago and it was believed Al Shabaab was using the area to launch strikes in Kenya.
"The combined security units discovered five different Al Shabaab hideouts inside the forest," the head of the operation, James ole Serian, told Reuters.
"The hideouts have already been destroyed and the weapons handed to the Government," he added.
None of the militants were arrested in the operation because they fled before it begun on September 11, he said. But several people in the surrounding area, mostly Kenyans, had been detained on suspicion of having links to the group, he added.
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"You will be seeing some of them in court soon," he said.
Military planes and helicopters have been sweeping the area since the operation began and local residents have reported sporadic sounds of gunfire and blasts from the area.
"We are not leaving Boni Forest any time soon, until we ascertain every terror element in the forest has been cleared," Mr Serian said, adding that the operation could take more than the three months originally planned.
Officials said at least 3,000 people living near the forest were forced to leave so that the operation could go ahead.
This comes at a time the US Government has placed a Sh1.4 billion bounty on the heads of six top Al Shabaab members.
Those wanted include Mahad Karate, also known as Abdirahman Mohamed Warsame, who has played a key role in the wing of Al Shabaab responsible for assassinations and the April 2 attack on Garissa University College.
Also wanted is Ahmed Iman Ali who recruited Kenyan youth and raised funds for Al Shabaab.
A reward of up to Sh600 million is being offered for information on the whereabouts of Al Shabaab's leader, Abu Ubaidah also known as Direye.
Mr Ubaidah was named head of Al Shabab in September last year after the group's long-time leader (Emir), Ahmed Abdi Godane, was killed in a US drone strike.
The US Department of State's Rewards for Justice Programme has also offered a reward of up to Sh500 million to anyone with information on the location of three other high-ranking leaders; Karate, Ma'alim Daud and Hassan Afgooye. Ma'alim Daud is responsible for Al Shabaab's planning, recruitment, training, and operations against the government of Somalia and Western targets.