Until now, the skulls have been stored at the Karolinska Institute in Stockholm, one of Europe's largest medical universities.
At the turn of the twentieth century, Swedish scientists investigating potential differences between races plundered numerous skulls belonging to groups including Maori – the indigenous people of New Zealand.
Many of the skulls were looted from graves and then measured and compared in order to try and classify differences between races.
Karolinska Institute has a collection of 800 skulls and since 2008, New Zealand's national museum Te Papa has been fighting to get three of them back.
Olof Ljungström, a historian at the Karolinska Institute, told The Local on Tuesday that he was aware the return of the skulls had taken longer than many had hoped, but insisted that they would be sent back to New Zealand soon, as part of a process that demanded "precision and care".
The transfer of the skulls needs to be formally approved by the Swedish state, which officially owns them. Ljungström said he felt there was a "great chance" that recent media interest in the skulls could help speed things up.
"People don't realize how complicated these processes can be. There's a lot of red tape and specific instructions to follow," he said.
He acknowledged that the Karolinska Institute had had a troublesome past with racial studies but added that there was a lot to learn from previous mistakes.
"Measuring skulls is morally indefensible, but we can't change the history. We can only learn from it and gain more knowledge."
It is understood that the three skulls were taken by Swedish zoologist Conrad Fristedt who visited New Zealand in 1890.
The collection has been lying untouched since the 1960s at Karolinska Institute, which first announced late last year that it was planning to return the remains to New Zealand.
Other bones and skulls stored in Sweden have already been flown back in recent years.
In 2011, the remains of three Maori people were returned at a solemn ceremony in Lund, in the south of Sweden.
They had originally been in London and ended up at the anatomical department and later the department of history at Lund University.