MasterChef contestant Ben Ungermann has been charged with two counts of sexual assault allegedly committed against a 16-year-old girl during a trip to Melbourne in February.

The Queensland cook disappeared from recent episodes of the hit Australian reality TV show, leaving viewers searching for answers.

Judge Jock Zonfrillo addressed the issue during Sunday night's episode, telling contestants: "You're probably wondering where Ben is. Due to a personal matter, Ben has had to leave the competition and he will not be returning."

In March, production company Endemol Shine released a statement saying Ungermann had been removed from the cooking show because he had been arrested by police for what was described as an incident of a "personal nature".

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"We can confirm Ben Ungermann has left the MasterChef Australia competition. As this is a police matter, we will not be making further comment," the spokesman said at the time.

Following questions from news.com.au, Victoria Police said police laid charges on a Queensland man in March.

"Melbourne Sexual Offences and Child Abuse Investigation Team detectives have charged a man following an incident in the Docklands earlier this year," a Victoria Police spokeswoman said.

"The arrest follows an investigation into an alleged sexual assault in Docklands on 23 February. A 36-year-old Queensland man has been charged with two counts of sexual assault.

"He has been bailed to appear at the Melbourne Magistrates' Court on June 25."

A police spokeswoman later on Tuesday confirmed the alleged victim is a 16-year-old girl.

Ungermann's name appears twice on Melbourne Magistrates' Court's daily listings for June 25.

Victoria Police's Sexual Offences and Child Abuse Investigation Team is handling the case, according to the court list.

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A spokesperson for Melbourne Magistrates' Court told news.com.au both charges are "sexual-assault related".

Rumours had began to swirl about the ice cream cook's whereabouts after he was mysteriously absent from Thursday's episode, featuring Katy Perry.

He should have been on the gantry looking down at contestants but was absent. He then popped up in a "Masterclass" segment later in the episode which had been filmed at an earlier date.

Ungermann hasn't spoken publicly about the arrest yet but he did reply to a fan's comment on Instagram about how his exit would be covered by the show.

"I'm actually devastated," the fan wrote to Ungermann. "How do they edit you out?"

The former contestant replied: "That's up to MasterChef Australia. Appreciate the support."