In the parliamentary election of 1999, the FAP joined with Chaudhry's FLP as part of the People's Coalition, an electoral alliance which also included a number of smaller parties. The FLP, supported mostly by Indo-Fijians, sought partnerships with parties led by ethnic Fijians in order to broaden its support base. The FAP won ten seats in the 71-member House of Representatives, its best result ever. The FAP initially proposed Speed for Prime Minister, saying that she would be more acceptable to indigenous Fijians than Chaudhry. President Mara, however, persuaded her to accept Chaudhry as Prime Minister, pointing out that the FLP had won a majority - 37 seats - in its own right. Towards the end of 1999, Speed survived a challenge to her leadership of the FAP in a divisive High Court case, which resulted in backbencherRatu Tu'uakitau Cokanauto and his supporters splitting from the party.
The government of which the FAP was a part was deposed in the Fiji coup of 2000, instigated by George Speight. An election to restore democracy was held in 2001, but by this time many of its members had left to join the new Soqosoqo Duavata ni Lewenivanua of Laisenia Qarase. The FAP contested only 15 seats, on a platform of alleviating poverty through income-generating projects, reducing health costs and increasing education assistance for poor families, promoting indigenous Fijian culture, and increasing the participation rate of women at all levels of decision making. The party also attempted to make inroads into the Indo-Fijian electorate, accusing the United Fiji Party of promoting racism. The electorate was polarized to an extent not seen for more than a decade, however, with ethnic Fijians rallying behind the Soqosoqo Duavata ni Lewenivanua and its ally, the Conservative Alliance, and Indo-Fijians behind the FLP. All FAP candidates, including Speed, were defeated.