Macron told Algerian website TSA he was ready to order the skulls' return during a 12-hour visit to Algiers on Wednesday.
French and Algerian intellectuals have been calling for the restitution for several years.
The skulls were found by Algerian archaelogist and historian Ali Farid Belkadi in 2011 as he went through the museum's stocks.
He launched a petition calling for their return to their homeland but, despite the fact that MPs had voted the previous year for the return of more than a dozen mummified Maori heads to New Zealand, it was not successful.
There have been other appeals for the remains to be returned to be buried with honour since.
The skulls belong to Algerians who fought against French colonialism in the 1840s and 50s after a 10-year war of conquest that failed to put an end to resistance.
Among them are those of Sheikh Bouziane, who led a revolt in the south in 1847, his 15-year-old son and a man called Si-Moussa, who was believed to be a Muslim holy man.
After a four-month siege of the town of Abd-el-Kader, French troops killed at least 800 Algerians but took the three captive, later executing them on the public square and displaying their heads on pikes in the town of Biskra to discourage further insurgency.
It is not known when exactly the skulls were sent to France.
During this year's presidential election campaign, Macron caused a row in France when he called colonialism a "crime against humanity" during a visit to Algiers.
Algerian war veterans' minister Tayeb Zitouni recently said he had great hopes for the restitution, "given M Macron's declarations during his previous visit".
In another interview published Wednesday, Macron declared he was "not a hostage of the past" and said he wanted to "turn towards our future together".
Macron in Qatar Thursday
On Thursday Macron heads for Qatar, where he is to meet the emir, Sheikh Tamin bin Hamad al-Thani, and visit French troops at the headquarters of the US's Centcom, which manages operations against Islamist insurgents in the region.
A number of business deals are in the pipeline, including the possible sale of 12 new Rafale fighter planes manufactured by French company Dassault and the operation of the Doha metro by the Paris regional transport network, the RATP, and Keolis.