France has returned three colonial-era skulls held in a Paris museum to Madagascar, 128 years after they were taken to France, including one believed to be that of a Malagasy king killed by French troops.

The skull, presumed to be that of King Toera and two others from the Sakalava ethnic group, were formally handed over at a ceremony held at the French Culture Ministry on Tuesday.

France has sought to confront its colonial past by returning artefacts and human remains from its museums to their countries of origin.

French Culture Minister Rachida Dati described the return of the skulls that had been stored at the Museum of National History in Paris as a "historic event" between France and Madagascar.

"This ceremony also symbolises the completion of a historical, scientific, and memorial process between our two nations," she added.

Her Madagascar counterpart, Volamiranty Donna Mara, hailed the return of the skulls as "a significant moment for the Sakalava community and the nation," saying the remains had great cultural and emotional importance.

"They are not collectors' items; they are the invisible and indelible link that unites our present to our past," Mara said.

"Their absence has been - for more than a century, 128 years - an open wound in the hearts of the Big Island and particularly of the Sakalava community of Menabe," Mara added.

Mara said the Malagasy government plans to honour the remains in a tribute coinciding with the anniversary of King Toera's execution in late August 1897 at Ambiky during France's colonisation of the Indian Ocean island.