Later in 2001, Agboyibo was tried for defamation of Prime Minister Agbeyome Kodjo; he had allegedly defamed Kodjo in 1998 by saying that Kodjo had participated in organizing a militia group while he was director of the Lomé port. On 3 August 2001, Agboyibo was sentenced to six months in prison and was fined 100,000 CFA francs. On 23 August, the International Federation for Human Rights (FIDH) called for his release, saying that he had not received a fair trial and noting that the president of the court was also the ruling RPT's representative on the National Electoral Commission. On 27 September, he was additionally charged with having links to a group that allegedly committed crimes in Sedome in 1997. In late November, Amnesty International called for Agboyibo's release. Although an appeal court ruled in favor of Agboyibo regarding the defamation sentence in January 2002, he was not released due to the other charge of criminal complicity. He was finally released on Eyadéma's orders on 14 March 2002, a decision that Eyadéma's office attributed to "the interest of national reconciliation and political appeasement". Agboyibo was the CAR's candidate in the presidential election of 1 June 2003, taking third place with 5.12% of the vote, according to official results. He claimed that fellow opposition candidate Emmanuel Bob-Akitani of the UFC won the election, placing Bob-Akitani's score at 54.80%, his own score at 13.46% (second place), and Eyadéma's score at only 11.03% (fourth place) in a statement on 4 June. Despite this claim, Eyadéma was officially declared the winner, and Agboyibo denounced the election as fraudulent. Regionally, Agboyibo was President of the Union of African Parties for Democracy and Development from 1996 to 2004 and became Vice-President of the Union of African Parties for Democracy and Development – West Africa in 2005. He was general coordinator of the opposition during the April 2005 presidential election; on 23 April, the day before the election, which was marked by violence and accusations of fraud, he denounced the election as "an electoral masquerade". On 22 April 2006 he was elected as the consensus choice for the position of President of the Bureau of the Inter-Togolese Dialogue, which ran from 21 April to 20 August 2006. His appointment as Prime Minister was announced on 16 September 2006 and he formed a government, composed of 35 ministers, four days later.