The 29-year-old Welshman finished 19th on the second stage, leaving him 54 seconds behind overall leader Nairo Quintana of Colombia.
Russia's Ilnur Zakarin outsprinted Quintana to take the stage win.
Tour de France champion Chris Froome was off the pace after suffering a puncture with 21km remaining.
Tour de Romandie, stage two:
1.  Ilnur Zakarin (Russia / Katusha)          4hrs 28mins 40secs
2.  Nairo Quintana (Colombia / Movistar)      Same time
3.  Rui Costa (Portugal / Lampre)             +26secs
4.  Rigoberto Uran (Colombia / Cannondale)
5.  Thibaut Pinot (France / FDJ)
6.  Jon Izagirre (Spain / Movistar)
7.  Rafal Majka (Poland / Tinkoff)
8.  Mathias Frank (Switzerland / IAM Cycling)
9.  Pierre Rolland (France / Cannondale)
10. Simon Spilak (Slovenia / Katusha)
11. Bauke Mollema (Netherlands / Trek)
Selected others:
19. Geraint Thomas (Britain / Team Sky)     +57secs
Overall classification:
1.  Nairo Quintana (Colombia / Movistar)      7hrs 02mins 09secs
2.  Ilnur Zakarin (Russia / Katusha)          +10secs
3.  Jon Izagirre (Spain / Movistar)           +16secs
4.  Thibaut Pinot (France / FDJ)              +28secs
5.  Rui Costa (Portugal / Lampre)             +32secs
6.  Mathias Frank (Switzerland / IAM Cycling) +33secs
7.  Simon Spilak (Slovenia / Katusha)         +38secs
8.  Pierre Rolland (France / Cannondale)      +39secs
9.  Bauke Mollema (Netherlands / Trek)        +40secs
10. Rigoberto Uran (Colombia / Cannondale)    +42secs
Selected others:
14. Geraint Thomas (Britain / Team Sky)     +58secs
Britain's Geraint Thomas slipped from third to 14th after the second stage of the six-day Tour de Romandie in Switzerland.