Mali's interim president and prime minister resigned on Wednesday, two days after they were arrested by the military, an aide to the vice president said.

Soldiers led by interim Vice President Assimi Goita, arrested President Bah Ndaw and Prime Minister Moctar Ouane and took them to a military base on Monday after a cabinet reshuffle in which two officers lost their posts.

The military's actions have jeopardised Mali's return to democracy following a coup last August and drawn condemnation from international powers.

"The president and his prime minister have resigned. Negotiations are ongoing for their liberation and the formation of a new government," said Baba Cisse, an aide to Goita, in comments sent to Reuters by the military.

The resignations came during a visit by a delegation from the Economic Community of West African State (ECOWAS), which is pressing to resolve the stand-off. During a meeting with Goita late on Tuesday, the delegation, led by former Nigerian President Goodluck Jonathan, raised the possibility of sanctions against the officers responsible for the takeover, said a military official who was present.

Mali's neighbours and international powers fear the political crisis could further destabilise a country that Islamist groups linked to al Qaeda and Islamic State have used as a launch pad for attacks across the region.

On Tuesday, Goita, who led the coup in August against President Ibrahim Boubacar Keita, said the president and prime minister had violated the transitional charter by failing to consult him about the new cabinet.

Goita promised that elections planned for next year at the end of the transitional period would go ahead.

He also accused the government of mishandling the situation in Mali, including a strike last week by the main union. The union said on Tuesday it would suspend the strike in light of the political crisis.