If found guilty, Dr Jonathan Fielden faces up to two years in jail and being placed on the Sex Offenders Register.
The 53-year-old, who is one of the most influential doctors in the NHS, has already had conditions imposed on his practice by the Medical Practitioners Tribunal Service.
He now banned from working in any roles involving contact with patients.
However an NHS spokesman has confirmed that Dr Fielden is currently off work “for personal reasons.”
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An anaesthetist and intensive care specialist, he joined NHS England’s leadership a year ago.
His title is national deputy medical director and director of specialised commissioning at NHS England.
Bedfordshire Police have bailed Dr Feilden until March 23 while their enquiries continue.
Voyeurism, or ‘peeping Tom’ acts were made a criminal offences under the Sexual Offences Act of 2003.