In a statement read on state television on Friday, the public prosecutor in the capital Bangui said Martin Joseph Figueira had Portuguese and Belgian passports and had been detained on May 25 after an investigation was opened.
It did not give details of the charges but accused Figueira of being in contact with armed groups.
FHI 360, the public health NGO for which Figueira worked, according to the prosecutor, did not immediately reply to a request for comment. The Portuguese foreign ministry also did not respond.
Central African Republic, a former French colony and one of the world's poorest countries, has become a close Russian ally in recent years, hosting one of the Wagner Group mercenary army's largest foreign operations.
Violence waned there after a peace accord in February 2019 between the government and 14 armed groups, but the situation remains volatile as swathes of territory are still outside government control.