Around 3500 riders were taking part in the 81-mile event - the only sportive in the UK with a complete road closure - around Pitlochry, Perthshire, Scotland. It was reported that some riders came off their bikes after running over the tacks. The event restarted after the road was cleared.
Organisers are working with the police to determine the source of the tacks.
The popular event has met with resistance from some local residents, who object to the road closures. A campaign group called ACRE (Anti Closed Road Events) has been lobbying the local council to keep the roads open on the day of the Etape.
But a spokesman for ACRE, Peter Hounam, denied any involvement in the incident.
"We do not condone what happened today," Hounam told BikeRadar. "ACRE has always actively discouraged any suggestions of illegal direct action. As far as I am aware this is a rare occurrence in the world of cycling, and it is only one example of the anger people feel here that a commercial cycle race, and I mean race, can be staged here on closed roads.
"All over the country proper trial type events are run for charity, not profit, on open roads, and we would welcome one here. We have offered to marshall such an event if Perth and Kinross Council would get out of bed with the London-based multi-national behind Etape Caledonia and start supporting sustainable tourism events that the local community can get behind."