Cavendish took part in the sixty lap indoor race but lost touch as a group of six got away after sprinting well and was nowhere near the podium places come the end of the race won by Morgan Kneisky. He finished seventh one lap behind.
The Colombia High Road rider, who has has six road race victories this season already, will also race in the Madison on Saturday evening.
Britain's first gold medal of the Championship came in Women's Team Pursuit with victory against New Zealand in the final. Wendy Houvenaghel who won a silver last night was part of the three lady team along with Jo Rowsell and Liz Armitstead.
In the Women's Team Sprint, Vicky Pendleton and Shanaze Reade won silver medals.