Authorities in Mayotte are expected to launch Operation Wuambushu ("Take Back") next week to remove illegal migrants who have settled in slums on the island.
Those without papers are to be sent back to the Comoran island of Anjouan, 70 kilometers away.
"The Comoros do not intend to welcome people expelled as part of the operation planned by the French government in Mayotte," government spokesman Houmed Msaidie told AFP.
Msaidie said the planned action went against "the spirit and the letter" of agreements between the two countries.
Moroni earlier urged Paris to drop the operation, which was approved by French President Emmanuel Macron in February.
Mayotte and the three islands of the present-day Comoros were French territories until 1975.
Following a referendum, Grande Comore, Moheli and Anjouan islands declared themselves to be a separate country, the Union of the Comoros.
But Mayotte voted to remain a French overseas territory and later became a French department - a status rejected by the Comoros, which continues to claim the island.
Mayotte is France's poorest department with around 80 percent of the population living beneath the poverty line and high levels of social delinquency.
But it also benefits from French infrastructure support and welfare, and this has caused an influx from the Comoros, with many migrants attempting the hazardous crossing on rickety boats used by smugglers.