The world time trial champion suffered a puncture on the 41.5 km route from Arc et Senans to Besancon, just like he did in the opening time trial in the Tour prologue when he was again expected to shine.
"I'm really disappointed, I lost my rhythm. At the end it wasn't too bad but I could have fought for victory," the Omega Pharma - QuickStep rider told reporters.
Martin had more misfortune on the first stage last week when he broke a bone in his wrist in a nasty crash which also left his elbows bloodied.
He has continued to race with a specially made plastic cast on his wrist and the one bright spot of his situation is that he expects it to heal sufficiently enough for him to go for gold at the London Olympic time trial on August 1.
Going over a pothole on Monday though did not help.
"I suffered yes, it was very painful," he added.
Martin will decide later on Monday or on Tuesday's rest day whether to continue with the Tour or rest ahead of the Games.
Broken bones and accidents have been a feature of his season.
In April, he fractured his shoulder blade, upper arm and facial bones when he was hit by a car during a training ride.