Yuhanie had refused to let her son leave, telling her family he was the victm of black magic and demanded $6 million for his release.
Photographs emerged in April of Simon chained to a bed at his mother's house.
The Donaldson family asked Prime Minister John Key to raise Simon's plight with Indonesian officials while on a trade mission there in April.
Key said Ambassador David Taylor had met two Indonesian ministers to discuss the case.
Donaldson said Simon was moved on Wednesday to Dr Soetomo Hospital in Surabaya, where he would be assessed to see whether he was well enough to be deported.
"We are indeed relieved that he is now going to get medical help for his condition and the end aim here is that in a few months' time he will be fit to travel to New Zealand to continue the treatment at Omahanui with his brother Robin," said Donaldson.
Neither Yuhanie nor her lawyer responded to questions.