Paraguay authorities have launched a judicial investigation after the discovery of human skulls and skeletons of several people at the home of the deposed president of Paraguay, Alfredo Stroesner, who has run the country for more than 30 years.

The discovery of the remains came after homeless people found shelter in the dictator's former summer house and found human skulls on Wednesday under an old bathroom.

Ciudad del Este city prosecutor Alcides Jimenez said more remains are likely to be discovered in the house and surrounding land, and the special research team will begin work on the 12-hectare site starting next Tuesday.

The Truth and Justice Commission held the late dictator responsible for more than 20,000 human rights violations, including arbitrary arrests and executions, as well as abductions and torture.

Stroessner was ousted in 1989 and left the country to spend the remainder of his life in isolation in Brazil, where he died in 2006 from surgery.