General Sekouba Konate is expected to depart from Conakry for Senegal's capital.
Authorities with Senegal's government say Mr. Konate is due to arrive at a military hospital in Dakar, where he will be treated for a liver problem. It is unclear if Mr. Konate will be hospitalized or how long he will stay in Senegal.
Earlier this week, the interim leader announced plans to create a new civilian-led transition government in Guinea and said it would be led by a prime minister chosen by the opposition.
He said the country would move ahead with the transition while it waits for junta chief Moussa Dadis Camara to recover from an assassination attempt.
Camara was shot in the head by one of his aides in early December and rushed to a Moroccan hospital.
Guinea's ruling junta took control in an unopposed coup on December 23, 2008, shortly after the death of President Lansana Conte, who had ruled Guinea for decades.
Some information for this report was provided by AP..