The Etixx-Quick-Step rider touched the wheel of a Europcar rider in the closing moments and tangled with reigning champion Vincenzi Nibali (Astana) before going down.
The German was seen clutching his left shoulder afterwards and was immediately sent for an x-ray.
Dismay at the late crash was tempered a little when teammate Zdenek Stybar claimed the win on the brutal uphill finish into Le Havre, following 190 kilometres of hard racing from Abbeville.
“The stage on the cobbles was actually my goal. That I wanted to win,” said the stage winner. That did not work, but here I could do it. And that makes everything right.”
Stybar’s surge up the final kilometre was too much for the others, though runner-up Peter Sagan (Tinkoff Saxo) made a late lunge.
He just edged out Bryan Coquard of Europcar on a day that saw no change in the overall classification.
Froome is still second while Tejay Van Garderen (BMC Racing Team) is third. Martin,with the help of a swarm of teammates, crossed the line some minutes after Stybar.
However, rules stipulate that any crashes inside the final three kilometres that result in time losses are declared void — so Martin, at the time of writing — is still in the race lead.
The Irish trio of Dan Martin (Garmin Cannondale), Nicolas Roche (Team Sky) and Sam Bennett (Bora Argon 18) failed to feature in the final yesterday, the latter two conceding over three minutes while Martin opted to roll in towards the back of the main bunch, thus losing no time on the stage winner.
Today’s 190.5km seventh stage is from Livarot to Fougeres with a bunch sprint the likely outcome as there’s just one category four climb early on.
Meanwhile, the Irish U23 team for the European Track Championships next week (July 14-19) was named yesterday with Cormac Clarke, Thomas Fallon, Mark Downey, Javan Nulty, Fintan Ryan, Sean Grimes and Eoin Mullen making up the men’s squad.
They will be spread across all events, with Mullen the man for the sprints.
Downey will probably take in the points race, since he medalled in the junior event last year, while the team pursuit squad will most likely be Nulty, Clarke, Fallon and one other.
Josie Knight is the sole U23 female selected and having won a silver in the junior pursuit at these championships last year she will be one to watch.