The Government has ordered an end to unauthorised police swoops outside mosques.
National security minister Chris Murungaru said it was illegal for police to arrest people going to or coming from mosques during Ramadhan.
He was responding to demands by the chairman of the Mombasa branch of Supreme Council of Muslims, Sheikh Juma Ngao, Mombasa mayor Taib Ali Taib and former Cabinet minister Sharrif Nassir, for an explanation regarding the raids.
But the minister warned that the Government would deal severely with those who threatened the country's security irrespective of religion.
Dr Murungaru's warning came as human rights groups accused the Government of allowing foreign security agents to torture, interrogate and violate the rights of Kenyans suspected of terrorism.
They claimed the Government had allowed the US Federal Bureau of Investigations (FBI) and Israeli security agents to harass families and relatives of terror suspects.
They were particularly concerned about the continued detention of Mr Mohammed Ali Saleh - being held in connection with last year's bombing of Paradise Hotel in Kikambala, Kilifi, where 23 people including five Israelis died. The groups told the Government to obey an October 24 court order for his release.
Family members and representatives of the Human Rights network group said the suspect's continued detention was meant to put pressure on him to reveal the whereabouts of his brother, Mr Swaleh Ali Swaleh Nabhan.
Mr Saleh's sister, Dr Farida Ali Saleh, said her brother was first arrested with their mother, Mrs Esha Abdalla Nabhan, on December 9, last year but she was released eight days later.
She said Mr Saleh was arrested on October 18, this year, and had been held incommunicado in various police stations.
The family accused a State counsel of lying to the court that Mr Saleh had been freed when he was still in custody.
"We are concerned that our Government is allowing foreign agents to torture our people in violation of our law and international human rights statues. Our research shows that the Government in collaboration with the US agents is harassing the family," said the group.
By allowing foreign security agents to interrogate and torture Mr Saleh and other terror suspects, the Government was surrendering its independence - an affront to the dignity of the country as a sovereign State, they said.
"We doubt if US and Israel would allow Kenyan police to interrogate their citizens in their own countries," they said in a statement signed by representatives from People Against Torture, Release Political Prisoners, Independent Medico-Legal Unit, National Constitution Executive Council and Citizens for Justice, National Youth Movement.
The statement was read at a news conference at People Against Torture headquarters in Westlands, Nairobi.
Mrs Nabhan narrated how Israeli agents threatened her with torture if she did not disclose the whereabouts of her son.
She said she was suffering from depression following the re-arrest and detention of her son and urged the Government to release him.
Mr Saleh's wife, Muzdalifa, said she had visited many police stations in search of her husband without success.
She was accompanied by the couple's two children, Hamza and Haroon, and her brother-in-law Ibrahim Ali.