Thousands of people have been stuck on the Greek side of the border as Macedonian officials allow only a trickle of people through each day.
Frustration boiled over on Monday, with a few hundred people breaking through the gate, chanting "open the border" and throwing stones at Macedonian police, according to reports.
Police also used stun grenades to calm the crowd, Sky News reported, although there were no injuries or arrests reported.
Around 6,500 people have been stuck at or near the border crossing at Idomeni in Greece, with another 500 at a makeshift camp on a small concrete strip around 13 miles away.
Macedonia has previously said it will only allow in as many people as neighbouring Serbia agrees to accept but this has left thousands of migrants stuck in Greece.
Some have been there for up to eight days with little food or shelter.
Around 300 Syrians and Iraqis were allowed through the crossing between 11pm Sunday local time and 4am Monday but then Macedonian guards refused to admit any more.
The backlog has also stretched to Greece, where officials say more than 22,000 people are stranded.
Germany’s Chancellor Angela Merkel blamed Austria for the current build-up, after the country’s announcement that it would take no more than 80 asylum claims per day and cap the numbers of those seeking to cross the country.
This led to Macedonia refusing entry to Afghans and imposing stricter limits on Syrians and Iraqis, with Slovenia, Croatia and Serbia quickly following.