Souleymane Diallo, head of international competitions at the federation, told Algerian radio that the match, due to be played on June 12 in the capital Bamako, would "obviously" be moved "if the social and political situation remained the same".
But he added: "We're not at that stage. There's still more than two months to go before the fixture."
A group of low-ranking soldiers on Thursday overthrew president Amadou Toumani Toure, maintaining that the take-over was sparked by the government's inability to deal with a Tuareg-led insurrection in the north.
Diallo, however, said he did not think that the developments would affect the team's preparations for the match.
Algeria and Mali are in Group H of the second round of qualifying in Africa for the World Cup, which will take place in Brazil in two years' time. Rwanda and Benin are also in the same group.
Mali, who were third in the last Africa Cup of Nations, take on Benin away in a match scheduled to be played between June 1 and 5 while Algeria play Rwanda at home.
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