In 1993, he was elected to the National Assembly as a Deputy of the Militants for the Progress of Madagascar (MFM) for the Ikalamavony district, winning 57% of the vote.
[1] In March 2002,[2] during the conflicts following the December 2001 presidential election, Rakotoniaina was named President of the Special Delegation (Governor) of Fianarantsoa Province by Marc Ravalomanana.
Rakotoniaina attempted to hold on to power for several days, without success;[6] objecting to his dismissal, he said: "No one, at any level of this regime, can claim to have done more for President Ravalomanana than I have.
[9] General Andrianafidisoa (Fidy), to whom Rakotoniaina is considered close, allegedly attempted a coup in November 2006, two weeks before the December 2006 presidential election.
[13] A few days after the election, the authorities attempted to arrest Rakotoniaina, surrounding his home at night, but he was not present and was thought to be in hiding.
He had allegedly held a gathering on December 2, after the legal period for campaigning had ended,[14] misused public property, and made death threats against officials and police officers.
Opposition leader Andry Rajoelina then took over as President of the High Authority of the Transition and promptly pardoned Rakotoniaina, along with many other political prisoners (including Andrianafidisoa), on 26 March 2009.