Algerian President Abdelmadjid Tebboune announced the move on Thursday, the state-run Algeria Press Service reported, and French media reported they arrived in the Algerian capital, Algiers, on Friday afternoon.
France colonized Algeria from 1830 until its independence in 1962, following a seven-year war, but resistance to the occupation flared up on numerous occasions throughout the previous century.
The remains of several leaders of the resistance movements are among those being returned, the President said.
They include allies of Emir Abdelkader, an Islamic preacher who led a group of tribesmen in a lengthy struggle against French forces in the mid-19th century.
“Algeria is determined to bring the remains of other deported martyrs back to their homeland,” Tebboune said in a statement reported by APS.
He added that the move “perfectly mirrors our sacred respect for our martyrs and symbols of our Revolution, and our commitment to never give up any part of our historical and cultural heritage.”
French President Emmanuel Macron first said he was ready to return a number of skulls taken from Algerian resistance fighters on his first visit to the country in 2017, local media reported at the time.
“I wanted to engage France in a historic and ambitious reform of cooperation between the West African economic and monetary union and our country. We do it for African youth,” Macron wrote at the time.
Recent anti-racism protests have forced a number of major European countries to confront their colonial pasts, with many campaigners urging that statues and other public celebrations of imperialism be removed.