The current time trial world champion won the event in 15:58 minutes but that time was 38 seconds shy of Dowsett's record on the course held on the A63 between North Ferriby and North Cave.
Wiggins ended his career with Team Sky following the Paris-Roubaix in April and announced that he would attempt to break the Hour Record on June 7 at London's 2012 Olympic velodrome, Lee Valley VeloPark.
Dowsett, who races on the road for Movistar, recently set a new Hour Record on 52.937km on May 4 at the Manchester Velodrome. Although Wiggins complimented Dowsett’s performance as fantastic, he also told The Times that he could "break that record tomorrow."
Wiggins said that he hopes to set a new Hour Record that will stand for the next 20 years and suggested that 55 kilometres was a realistic target.
Dowsett is currently racing at the Bayern Rundfahrt where he won the stage 4 time trial on Saturday and moved into the overall race lead.
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