Thomas, who was recruited to the Dockers as a Category B rookie via its Next Generation Academy in November, was stopped by officers in Kununurra after he was granted permission to stay over the weekend following a community camp in the Kimberley.
"Whilst only having just joined the club, we value Leno very highly as a part of the Fremantle family and will work closely with him to ensure he is able to uphold the standards expected of both an AFL player as well as the broader community," Fremantle footy boss Peter Bell said.
"We are confident he will learn valuable lessons from this incident."