A court has criticised the role of federal police as it quashed the conviction of a charter pilot over the sexual assault of a teenage girl in Papua New Guinea.

Frederic Arthur Martens, 60, of Cairns, was sentenced to five years' jail by a Queensland court in October 2006 for the sexual assault of a 14-year-old girl in 2001.

In April, federal Attorney-General Robert McClelland ordered the case be referred to the Queensland Court of Appeal after new evidence came to light, and Martens was granted bail.

The evidence revolves around an affidavit from a family member of the girl saying the teenager told her in November 2003 she had been pressured to make up the allegation by Martens' former partner.

Martens also argued that he was 1000 kilometres away from Port Moresby on the night he was accused of raping the girl, and was adamant that civil aviation records backed this up.