A Perth court has been told a 28-year-old man intends to plead not guilty to murdering another man whose head was found washed up on Rottnest Island.

Aaron Carlino is accused of murdering Stephen Cookson, 56, in December last year.

It is alleged he shot Mr Cookson at an East Perth apartment and then disposed of the body with the help of an unidentified associate.

A young girl then found the head in a plastic bag on a Rottnest beach in January.

Prosecutors told the Stirling Gardens Magistrates Court they had a seven and a half hour confession from Carlino but his lawyer said he would be defending the charge.

The court has also been told investigations are still continuing into whether the second person will be charged over the murder.

Carlino is due back in court in July.