The Team Sky rider was down to ride both the time trial on Thursday and the road race on Sunday but his name has been removed from both start lists. Team Sky have not yet responded to Cyclingnews' request for a reason for the withdrawal.
Thomas would have been well suited to both races, but in particular the road race, which features part of the Lincoln Grand Prix circuit, with nine trips up Michaelgate – a cobbled climb of 300 metres with a gradient of 12 per cent.
The Welshman's absence in the time trial widens the door for three-time champion Alex Dowsett, the only WorldTour rider on the entry list, and multiple-time podium finisher Matt Bottrill (Drag2Zero).
Thomas recently rode to second overall at the Tour de Suisse, where he managed to climb with the best on the queen stage to the Rettenbach glacier. He narrowly missed out on taking the overall victory to Katusha's Simon Špilak in the final time trial. The result followed a successful Spring Classics campaign, during which he won E3 Harelbeke, and strong early-season showings at the Volta ao Algarve and Paris-Nice.
Thomas is almost certain to be named in Sky's nine-man Tour de France line-up, set to be announced on Monday, not least for his value in a potentially chaotic opening week and in the team time trial on stage 9. The decision may be based on his Tour preparations.
Team Sky will be well represented in the road race, with defending champion Peter Kennaugh joined by Andy Fenn, Luke Rowe and Ian Stannard.
Click here to see the elite men's and women's start lists for Thursday's time trial