Latortue, installed as the head of an interim government after bloody street protests drove Aristide into exile in February, made the announcement on Friday as he formed a committee to investigate misappropriation of public funds by the deposed government.
"I gave Justice Minister Bernard Gousse the order and I expect the warrant to be issued," Latortue said.
Latortue and other Haitian officials have publicly accused Aristide of corruption, but no charges have been filed and no evidence made public against the former president.
Under Haitian law, only judges have the power to issue arrest warrants.
"This is something we should have done a long time ago and the time has come," Latortue said, calling on the international community to cooperate with Haiti's interim authorities in the fight against corruption.
Latortue appointed a five-member investigation committee to investigate the Aristide government from the beginning of his term in February 2001 to his departure in February this year.
Aristide is in exile in South Africa after violent street protests and pressure from United States and France forced him to leave Haiti.