One report claimed at least 12 women were abducted during the latest attack on Kenya’s coast, which also left at least 15 people dead.
President Uhuru Kenyatta has blamed “local political networks” for the overnight raids on two villages near the town of Mpeketoni.
Meanwhile, Somalia’s al-Shabab group said it had carried out the attacks.
In a nationally televised address, Uhuru Kenyatta said that despite claims of responsibility from al-Shabab, the Islamist extremists were not behind it.
The Somali militant group had claimed responsibility for two nights of attacks near the tourist resort island of Lamu that targeted non-Muslims.
The latest attack came on Monday night in Majembeni village. The village is next to Mpeketoni, where four dozen Christian men were killed on Sunday night and Monday morning.
Al-Shabab said the second attack killed government workers and Christians. A county commissioner, Benson Maisori, said the attackers appear to have been the same in both cases.
“The style of killing is the same. They slit the victims’ throats wide open or shot them several times in the head,” said Mr Maisori.
But in a surprising turn of events, Mr Kenyatta said outright that al-Shabab did not plan and execute what he termed ethnically motivated violence, but rather local political leaders were responsible. He said police officials in Mpeketoni had advance intelligence about the attack but did not act on it. The president said some officers had been suspended and would be prosecuted.
Mr Kenyatta said some political leaders were preaching the idea that some Kenyans were less human than others. “My deputy and I will never go the route of ethnic violence,” he added.
The attacks underscore the weak security around the Lamu area, which lies just south of the Somali border. Lamu once attracted swarms of foreign visitors but its tourist sector has been suffering in recent years because of the violence.
Interior minister Joseph Ole Lenku said a new slate of government and security officials have been installed in Lamu, in part because “there seems to be some inside job”.
Mr Ole Lenku said the problem facing the country “is elaborate and is intended to cause discord among our people”.
Meanwhile, Muslim leaders conferred inside Nairobi’s largest mosque. The elders from four different groups condemned what they called savage acts and ghastly killings and said there was no justification for the deaths.
The Muslims leaders warned of a potential sectarian rift.
“The continued violence risks tearing the country apart,” they said. “We need to be cognisant of the fact that some of these attacks are aimed at planning seeds of discord and animosity among Kenyans and dividing the country along ethnic and religious lines.”
The Muslim leaders said the government is taking “knee-jerk reactions” and harassing specific communities, a reference to Kenya’s Somali population, which has suffered in a widespread crackdown in the last few months which has seen the arrests of thousands of Somalis and the deportation of dozens.