The country has been under military rule since back-to-back coups in 2020 and 2021, with the security situation compounded by a humanitarian and political crisis.
The coalition, named "Action Synergy for Mali," was set up in February and is made up of 30 opposition parties including supporters of an influential imam, Mahmoud Dicko.
"Due to the security situation and the risk of threats to public order, the activities of the 'Action Synergy for Mali' group are formally banned throughout the entire district of Bamako," said a decree dated on Monday from the capital's governor Abdoulaye Coulibaly.
The coalition rejected the ban, describing it as an "illegitimate and illegal decision that violates the freedom of association and expression guaranteed by the constitution."
The group is highly critical of the junta and has proposed "a new way" for Malians who have seen the country ravaged by different groups affiliated with Al-Qaeda and the Islamic State group since 2012.
"Expectations of the people were far from being met," the coalition has said.
The governor pointed to "multiple actions" by the coalition that he said were in "violation of current regulations."
In mid-March, the United Nations said it was "deeply concerned" by the dissolution of civil society organisations and "increasing restrictions" on human rights and fundamental freedoms in Mali.
At least four organisations have been dissolved since December 2023, including groups relating to good governance, elections and opposition, a UN spokesperson said in a statement.