Mali's military rulers said on Monday that Ecowas representative Hamidou Boly was "persona non grata" and gave him 72 hours to leave the country.
Foreign minister Abdoulaye Diop told local television that Boly had engaged with groups that "undertake activities hostile to the transition".
Mali's interim government has said that it will set an election date after holding a "national forum on rebuilding" in December.
West Africa bloc Ecowas on Thursday branded Mali's recent expulsion of its representative as "extreme," and said it would continue pushing for a transition to civilian rule in the Sahel state.
Mali's military rulers said on Monday that Ecowas representative Hamidou Boly was "persona non grata" and gave him 72 hours to leave the country.
Foreign minister Abdoulaye Diop told local television that Boly had engaged with groups that "undertake activities hostile to the transition".
The expulsion came at a time of growing pressure on Mali's junta to stage elections -- from both the 15-nation Ecowas and the United Nations.
In a statement published on Thursday, Ecowas said that it "regretted the decision" to expel its envoy.
"This extreme decision comes at an important and delicate time when Ecowas and other partners are assisting the political transition," the statement said.
The Economic Community of West African States added that it would "stay engaged" and keep pushing for a peaceful transition to civilian rule.
Mali slid into political turmoil last year, culminating in a putsch led by Colonel Assimi Goita in August 2020 against president Ibrahim Boubacar Keita.
Under the threat of sanctions, the military then appointed an interim civilian government tasked with steering the country back to democratic rule.
But Goita overthrew the leaders of that interim government in May -- in a second putsch -- and was later declared interim president himself, drawing international condemnation.
Mali's interim government has said that it will set an election date after holding a "national forum on rebuilding" in December.
Swathes of the vast nation of 19 million people lie outside of government control because of a jihadist insurgency that first emerged in the north in 2012, before spreading to the centre of the country, as well as neighbouring Burkina Faso and Niger.