The majority of the 22 skulls were taken from burial sites in the Pacific islands by Swedish scientists in the 1880's. The museum received five skulls through a donation in 1997, while the other 17 were found at Stockholm's medical university Karolinska Institutet.
Museum director Lars Amreus said he hoped that the skulls' return would help "fullfill the spiritual circle" of those whose graves had been violated by the scientists.
The head of the delegation from Hawaii, William Aila, was moved by the return.
" I cannot adequately express the thankfulness for a very, very worthy endeavor, and that is to greet our ancestors and accompany them home," Aila said in a speech during the ceremony. He added that the skulls would be "reburied in the soil of their birth," back in Hawaii.
On Wednesday Sweden will return to New Zealand a near complete skeleton, a skull and three skeleton parts all belived to have been from the indigenous Maori population.