The Netherlands has returned four pieces from a major archaeological collection to Indonesia, including the skullcap which provided the first evidence of an extinct human species.

The so-called Dubois collection consists of some 28,000 fossils and had been held in the Netherlands for more than a century.

On Wednesday, the Naturalis museum in Leiden said four fossils – the skull cap, a molar and thigh bone from homo erectus, and a scratched shell – had been returned personally by museum director Marcel Beukeboom.

All four have been replaced on display by yellow plastic copies to show they are replicas. The remaining fossils will be returned next year.

The “Java man” fossils were initially dismissed as apes’ bones, but later recognised as belonging to one of the extinct human species that lived alongside early homo sapiens. In the late 19th century, the find was hailed as the “missing link” in human evolution, as envisaged by Charles Darwin.

It is the sixth time that the Dutch government has acted on a special government commission’s advice to repatriate objects. Earlier this year, 113 bronze statues were returned to Nigeria.

 The Dubois fossils remain important for science, and Naturalis in Leiden has been working with Indonesian researchers for years to study them. Indonesia formally requested their return in 2022.

The collection is expected to go on display at the National Museum in Jakarta.