A national manhunt started after video footage broadcast on Kenyan TV appeared to show an unidentified man assaulting an unconscious woman on a clinic bed.
Mugo wa Wairimu has denied the allegations and said the report was an evil plot by his enemies.
Kenya's Medical Practitioners' Board says he is not a registered doctor.
The accused man was arrested on Thursday at a hotel outside Nairobi after members of the public called the police.
They accused him of operating a number of clinics in Nairobi without a valid licence.
He was taken to court to be charged but the prosecution said investigations were not complete.
Mr Wairimu will be detained for two weeks while police carry out further enquiries.
The BBC's Odhiambo Joseph in Nairobi says the court was told that releasing Mr Wairimu might endanger his life because of growing public outrage, something his lawyers did not oppose.
Mr Warimu was not asked to enter a plea.
Four women have lodged official complaints with the police so far over claims of sexual abuse.
Citizen TV said on their report, which was broadcast on Sunday, that they do not know the identity of the woman in the video, which was filmed by a suspicious staff member, or if she is aware of the alleged assault.
A Kenyan man accused of posing as a gynaecologist and allegedly raping women in his clinic after sedating them has appeared in court in Nairobi.