In early February the Malagasy parliament passed a bill allowing chemical and surgical castration of people convicted of raping minors.
Amnesty International condemned the measure as "cruel, inhuman and degrading."
A few weeks later, the European Union's ambassador, Isabelle Delattre Burger, who has been critical of the government in the past, blasted the measure during a press conference.
The measure is "contrary even to the Madagascar constitution" and to international norms, Burger said.
Burger was summoned to Madagascar’s foreign ministry following the remarks.
On Thursday, a spokeswoman for the European Commission said Madagascar called on Brussels to replace the envoy.
"Madagascar foreign affairs minister addressed a letter to the high commissioner to express his dissatisfaction... and to ask the EU proceed to replace the head of its delegation," Nabila Massrali, told AFP by telephone from Brussels.
The EU is studying the demand "in consultation with the Malagasy government," she said, adding that regular ambassador rotations are due to take place in September.
Clara Randrianjara, the head of communications for the Madagascar foreign affairs ministry, said "this letter should have remained confidential" and declined to comment further.
The EU is one of the main donors to Madagascar, which heavily depends on international aid and where nearly 75 percent of the 29 million-strong population live in poverty.
At the end of February, Madagascar’s High Constitutional Court validated the surgical castration portion of the controversial bill but excluded chemical castration because of its "temporary and reversible character" that would not "permanently neutralize sexual predators."