The two West African countries are run by military juntas that seized power in coups and have been taking steps to distance themselves from France, their former colonial ruler, despite previous close partnerships in security and other areas.
The statement revoked one agreement with France from 1972 which was meant to avoid double taxation and "establish rules of reciprocal assistance" in various tax matters.
The other agreement had similar aims.
"The persistent hostile attitude of France against our states... added to the unbalanced character of these agreements causing a considerable shortfall for Mali and Niger," said the joint statement, which was shared by Mali's foreign ministry on social media.
There was no immediate reaction from Paris.
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