More than 3,500 people were taking part in the Etape Caledonia, over 81 miles around Pitlochry in Perthshire.
It is the only cycle event in Britain where all the roads travelled on are closed - which has angered some locals.
Tacks were strewn on a section of the race, bursting hundreds of tyres. Police said it was a reckless act and it was fortunate no-one was hurt.
Cyclists ended up with damaged tyres and the event had to be stopped but organisers cleared the road and the race was completed.
The winner Veli-Matti Raikkonen - who is originally from Finland and is a member of Aberdeen's Granite City racing team - was one of those who suffered a puncture after riding over the tacks.
A spokeswoman for the race said organisers were now working with Tayside Police to discover what had happened.
Some campaigners are angry because they believe their freedom of movement is being restricted, visitors may be put off coming to the area, affecting tourism and business, and locals could be prevented from getting to church.
Peter Hounam, from the Anti Closed Road Event (Acre) group, said: "Acre is against the closure of roads for cycle events in our area, we do not object to cyclists or people taking part in events.
"We totally deplore anyone taking direct action and we want people to have peaceful protests.
"We don't condone what has happened, but it shows there is real frustration from people who feel the authorities are not listening to them."
He said the event discouraged tourists because of the road closures and that it did not bring the kind of sustainable tourism needed in Perthshire, as many of the participants only stayed overnight.
But Kathy James, who runs a bed and breakfast in Aberfeldy, said the race brings millions of pounds to the area.
She told BBC Scotland: "What they've done is they've spread, from Rannoch down to us, tiny, tiny carpet tacks - I've got one - they've just spread the road with them.
"There's a chap outside who came off his bike, there's been a lot of people coming off their bikes and basically they had to stop the race further up.
"This area relies on tourism, it disgusts me as a local, I just think there's no logic behind it."
Source: BBC News/UK