The Whitecaps released a short statement with the announcement after a story appeared on Goal.com that said Lewis had signed with the Cosmos of the second-tier league. A Cosmos spokesman confirmed that story with The Canadian Press.
Whitecaps team president Bob Lenarduzzi said Lewis will be at pre-season training and that the issue is being dealt with by Major League Soccer and the Cosmos.
"He's going to be in Vancouver," said Lenarduzzi. "He's our player."
Whitecaps head coach Carl Robinson said the team was aware of the situation before drafting Lewis.
"We knew about that," said the rookie coach. "I wanted good players in my team and that's why we picked him."
The Whitecaps selected Lewis with the seventh pick in Thursday's MLS SuperDraft. He seemed thrilled by the news when he spoke to reporters on a conference call after the draft.
"I'm a fan of Vancouver because of Darren Mattocks," said Lewis, referencing the Whitecaps striker and fellow Jamaican. "I love the support that the fans give to Vancouver. I'm looking forward to starting my professional career with the Whitecaps and to just go there and work hard and do my best."
The five-foot-nine 145-pound Lewis represented his country at the under-17 and under-20 levels before earning his first senior call up in 2012.
"On the pitch, I always want to be a top player," said Lewis on Thursday's conference call. "Win or lose, I want to be on top of my game at all times."