Thirty-five people were arrested, the Pas-de-Calais prefecture said, according to CNN affiliate BFMTV.
The prefecture said that 24 of those arrested are migrants and 11 are members of the pro-migrant activist group No Borders, according to BFMTV. About 110 migrants were removed from the port zone.
The incident disrupted ferry traffic between Calais and Dover, England, for up to two hours, the British firm P&O Ferries said via Twitter.
The port was temporarily closed, according to a Twitter post by another British ferry company, DFDS Seaways.
"Once again, there is proof that demonstrations organized by pseudo-migrant defenders have essentially aimed to disrupt economic life," Mayor Natacha Bouchart said on Facebook.
Earlier in the day, an authorized demonstration organized by migrant supporters took place in downtown Calais and was marked by some incidents, Bouchart said.
Some 2,000 people took part in the demonstration, according to French media outlets.
An estimated 6,000 migrants and refugees have been living in one of Europe's most famous refugee camps, the so-called "Jungle," near Calais, trying to make their way illegally into the United Kingdom, with the hope of a better life.
The "Jungle" has become a massive sprawling campsite on waste ground, where migrants and refugees have been living in grim and unsanitary conditions.
Lately, French authorities have been trying to clear some areas within the "Jungle" and move some people into shelters made out of metal shipping containers equipped with heaters and electricity.
A French member of the European Parliament who took part in the demonstration called on the French government to fix the situation.
"We cannot let the situation here continue. These people are living in unacceptable conditions. I call on (French Prime Minister) Manuel Valls, on (Interior Minister Bernard) Cazeneuve to do whatever is necessary to fix the situation, and in the first place, that the people here have acceptable living conditions -- housing, proper food, but above all clothing, because these conditions are really inadmissible. It's like an open-air prison. It's a question of dignity, we can't allow this," Green Party politician and MEP Karima Delli told reporters.