Reports suggested the 27-year-old fell while crossing a train track and was run over by a bus travelling behind him.
A team statement read: "IAM Cycling have lost Kristof Goddaert, an exemplary professional rider and a man of quality. We always appreciated his good humour every day, his enthusiasm and his full commitment to whatever he attempted.
"Our thoughts are with his family and those close to him, and we send them our condolences at this terrible time."
Britain's track and road world champion, and 25-time Tour de France stage winner Mark Cavendish wrote on Twitter: "Just read the tragic news about Kristof Goddaert & brought to tears. Such a nice guy who loved racing his bike. RIP Kristof." Goddaert was third in the Paris-Brussels road race in 2009 and second in the 2008 Tour de Vendee, as well as winning a stage of 2010's Tour de Wallonie.
His death follows that of South African racer Jeanne Nell, who died following a racing crash in Cape Town last Tuesday.