Mali could be thrown out of the 2018 World Cup qualifying competition after the government sacked the national football federation leaders.
The bottom-of-the-table west Africans are scheduled to play Morocco twice, group leaders Ivory Coast and Gabon this year.
Global football body FIFA does not permit government interference in the sport, resulting in a number of African countries being banned previously.
"The ministerial decision goes against (the independence of the member associations)," a FIFA statement said.
"In case the decision is not cancelled on Friday March 10, the case would automatically be submitted to the FIFA Council bureau for consideration."
Despite the threat, the Malian sports ministry remained defiant Saturday, saying they want to end "persistent crisis in football.
"It is a government decision and it will not be reversed," said sports ministry lawyer Amadou Diarra Yalcouye.
"FIFA cannot oblige the government to reverse its decision.
"The sports ministry will soon set up a committee tasked with reuniting the football family."
Mali performed poorly at the 2017 Africa Cup of Nations in Gabon, scoring only one goal as they lost to Ghana and drew with Egypt and Uganda.
The country is ranked 12th in Africa and 61st in the world.