The Etixx Quick-Step rider fell after touching wheels with the cyclist in front of him and brought down fellow general classification favorites Vincenzo Nibali (Astana Pro Team) and Nairo Quintana (Team Movistar).
Zdenek Stybar, Martin’s team mate, was able to escape the crash and coasted to victory in a time of four hours and 53 minutes.
Martin was able to finish the race with the assistance of a team mate, but appeared to have damaged his collarbone and clutched his left arm all the way to a finish line. It is not yet known whether he will line up for the next stage.
The German now leads the general classification by 12 seconds, with Great Britain’s Chris Froome (Team Sky) in second place.
Stage 6 results
1. Zdenek Stybar (Cz) Etixx – Quick-Step 4hrs 53 mins
2. Peter Sagan (Slo) Tinkoff – Saxo 2 seconds
3. Bryan Coquard (Fra) Europcar same time
4. John Degenkolb (Ger) Giant
5. Greg Van Avermaet (Bel) BMC Racing
6. Tony Gallopin (Fra) Lotto
7. Edvald Boasson Hagen (Nor) Team MTN
8. Davide Cimolai (Ita) Lampre
9. Julien Simon (Fra) Cofidis
10. Gorka Izagirre (Esp) Movistar
1. Tony Martin (Ger) Etixx – Quick-Step 22hrs 13mins 12secs
2. Chris Froome (GB) Team Sky 12secs
3. Tejay van Garderen (US) BMC Racing 25secs
4. Peter Sagan (Svk) Tinkoff – Saxo 27secs
5. Tony Gallopin (Fra) Lotto 38secs
6. Greg Van Avermaet (Bel) BMC Racing 40secs
7. Rigoberto Uran (Col) Etixx – Quick-Step 46secs
8. Alberto Contador (Spa) Tinkoff – Saxo 48secs
9. Zdenek Stybar (Cze) Etixx – Quick-Step 1min 06secs
10. Geraint Thomas (GB) Team Sky 1min 15secs