An Australian man and his Filipino girlfriend have pleaded not guilty to charges of raping and trafficking two girls aged 9 and 12 in a southern Philippine city.

Cagayan de Oro City Prosecutor Fidel Macauyag says Peter Gerald Scully and Carme Ann Alvarez were arraigned Tuesday on five counts of rape through sexual assault and one count of child trafficking. The trafficking charge is not bailable.

According to Macauyag, Alvarez invited the two girls to the couple's apartment, where they were allegedly held and abused for three days in September 2014 before they escaped and reported what had happened to their parents and the police.

Macauyag says Scully is also under investigation in the death of a girl whose remains were found inside his house in another southern province.