Melbourne Rebels rugby star Amanaki Mafi has been arrested in New Zealand.

Rugby Australia have confirmed that Mafi is in New Zealand police custody, and is facing charges after an alleged assault on his Rebels teammate and Wallabies player Lopeti Timani.

The Rebels last night missed out on making the Super Rugby playoffs following their 43-37 loss to the Highlanders in Dunedin, and afterwards it is alleged that Mafi - a Japanese international - was involved in an altercation with Timani.

Rugby Australia and the Rebels tonight issued a joint statement confirming the incident.

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"Rugby Australia and the Melbourne Rebels are aware of an incident involving Rebels players Amanaki Mafi and Lopeti Timani in Dunedin overnight."

"Both players remain in New Zealand with Mafi currently in police custody following an altercation between the two players.

"Rugby Australia understands that no other players were involved in the incident.

A New Zealand Police spokesperson confirmed that a 28-year-old man has been charged with injuring with intent to injure following the alleged assault.

The police confirmed the men involved in the altercation were known to each other.

"The alleged victim, also a 28-year-old man, received moderate injuries following the incident. He did not require hospitalisation," the spokesperson noted.

Melbourne Rebels chief executive Baden Stephenson was disappointed with the news.

"I am bitterly disappointed that an incident has occurred at the end of a season where we have taken pride in our on and off field behaviour," Stephenson said.

Mafi has played 21 tests for Japan and was named Australia's Super Rugby player of the season last year.

It is understood Mafi will appear in the Dunedin District Court tomorrow.