Cavendish has not ridden an global team pursuit for some time and his best of four minutes 08.345 seconds is from a World Cup event in Moscow in December 2005.
The Guardian's Helen Pidd, who is in Rio, said the Manxman, aged 31, had "thrown his toys out of the pram and refused to come down and warm up".
Cavendish will focus on the six-discipline omnium, targeting the Olympic medal that has proved elusive in the past two Games.
But Cavendish hinted at behind-the-scenes tensions this week, making public his frustration at likely not being given an opportunity in the 4km, four-man team pursuit, which has qualifying on Thursday and concludes on Friday with a semi-final and final.
Had Cavendish ridden the qualifying round last night, or in tonight's first round, he would be eligible for a medal should Team GB win one, and in theory he could ride this evening should another team member be injured or fall ill - assuming, that is, he could reach the velodrome in time.
RCUK prediction: A British gold medal in the team pursuit looked an absolute certainty until Australia bettered them in St.Quentin in 2015 and the wheels fell off at the 2016 worlds.
Sir Bradley Wiggins at the Velodrome, Rio de Janeiro, Brazil August 11.
Bradley Wiggins, Edward Clancy, Steven Burke and Owain Doull set a new mark of 3min 50.570sec, taking more than a second off their time from London four years ago.
Before beginning his bid for a fifth Olympic gold and British record eighth medal in all, Wiggins showed annoyance at being summoned by commissaires.
Despite facing the prospect of being overtaken by Wiggins, Hoy has backed the former Tour de France victor to win another gold in the velodrome.
A poor qualification at March's Track World Championships - when Archibald was absent following an unauthorised motorbike accident which saw her sustain knee and elbow injuries - meant Britain could win bronze at best.
Still Cavendish is unlikely to be called upon.
"That's the reason I left the Tour early, because of the team pursuit", Cavendish told Sky Sports.
But speaking of the upcoming Omnium Cavendish said: "At the end of the day I qualified for the Olympics for the Omnium anyway, so I'll concentrate on the Omnium".
"(For) the omnium, finishing the Tour would've been a benefit. If something happens to them then I'll ride. That's what I was aiming for the whole time. "I'm kind of just doing the omnium stuff now, I think".