The case was filed at the HulhuMale Magistrate Court.
Nasheed and Tholhath stand charged with violating Article 81 of the Penal Code, which states that the detention of a government employee who has not been found guilty of a crime is illegal. If found guilty, Nasheed and Ibrahim will face a jail sentence or banishment for three years.
He said on Sunday that he was ready to face charges and to answer the case at the Court.
Nasheed is the second former President in country's history to be charged after late President Ibrahim Nasir, who was convicted for during the Presidency of Maumoon Abdul Gayoom.
Nasheed had put criminal court judge Abdulla Mohamed under military detention after the then government headed by Nasheed accused him of political bias, obstructing police, stalling cases, links with organised crime and "taking the entire criminal justice system in his fist" to protect key figures of the former dictatorship from human rights and corruption cases.
Despite pressures from both international and local parties and a direct order by the Supreme Court for his immediate release, judge Abdulla had been detained in a military training facility at Kaafu Atoll Girifushi for 22 days.
The detention was termed illegal as it failed to follow the procedure laid down to arrest a top government officials.