Rajab, who already faces 15 years in jail for his criticism of Manama's main ally Saudi Arabia, was accused of making comments that "harm the interests" of Bahrain and other Gulf countries, the official BNA news agency said Thursday.
It said the case had been transferred to the prosecutor's office and added that Rajab, a leading opposition activist and the founder of the Bahrain Centre for Human Rights, denied writing the article in question.
A piece published by Le Monde on Tuesday attributed to Rajab denounced the Islamic State group and accused Gulf nations of failing to tackle the rise of its violent ideology.
"Gulf states claim to be allies in the fight against extremism, but they are fuelling the crisis," the article said.
Rajab was arrested in June for comments on Twitter that criticised Saudi Arabia's role in military operations in Yemen, according to Human Rights Watch.
The court dealing with the case has repeatedly ordered that Rajab, 51, remain in custody despite recurring health problems for which he was briefly hospitalised in late June.
The next hearing in that trial is scheduled for December 28.
The Shiite activist has been detained several times since unrest in 2011 after security forces in the Sunni-ruled kingdom crushed protests calling for a constitutional monarchy and an elected prime minister.
Rajab was pardoned last year in another case for health reasons.
HRW on Thursday accused Bahrain of holding an engineer incommunicado for five weeks without access to his family or a lawyer.
The watchdog said authorities' failure to provide information on the whereabouts of Sayed Alawi, who was detained on October 24, constituted "an enforced disappearance".