"Niger is following with concern and total disapproval the evolution of the situation in Mali," a statement read out on state radio said, adding that Niamey "condemned all unconstitutional changes".
Rebel troops on Thursday seized key buildings in the capital and drove President Amadou Toumani Toure from his official residence.
Mali is usually seen as politically stable, but unrest in the north, where Tuareg tribes have long felt ignored by a southern government and where al-Qaeda has also taken root, has created a major security problem.
Junta spokesperson Lieutenant Amadou Konare said the takeover was because of a "lack of adequate [military] material to defend the nation".
In mid-January the Tuareg launched a fresh rebellion for the independence of what they call Azawad, which makes up the vast desert northern triangle of the nation.
The fighting has forced as many as 206 000 people to flee their homes, compounding a humanitarian disaster at a time of drought and food shortages, according to the United Nations.