Mr Bambang Susantono, a former official at the Asian Development Bank who was heading the new capital project, was not immediately available for comment.
Mr Dhony Rahajoe, an Indonesian architect and former real estate developer who was the deputy head of authority, also did not immediately respond to a request for comment.
The resignations of the two professionals comes amid a lack of private funding for the ambitious new capital being built in a remote and jungled patch of Kalimantan, on the Indonesia part of Borneo island.
The government has been racing to build the infrastructure required for the relocation of the first batch of 12,000 civil servants this September. But the plan has previously been twice delayed, raising doubts about the president’s signature project.
Nusantara is regarded as a major legacy of Mr Widodo, who will step down this October after serving the maximum two terms in office.
Jokowi, as the president is known, plans to visit Nusantara on Tuesday to inaugurate several projects, including schools.
