The riot broke out on Thursday, when dozens of migrants were trying to leave the Harmanli center, but were met by police and firefighters who used water cannons against them. About 2,000 refugees then took part in the protest. Late Thursday's ministry statement said 40 people were detained.
"The situation in the Harmanli reception center is calm at the moment… Around 400 foreigners have been detained for attempted vandalism during yesterday's disturbances in Harmanli. Another 15 people have been detained for causing damage to camp property," the ministry said in a statement.
Over 20 law enforcement officers were injured in the clashes, the ministry said, adding that police had to use water cannons and rubber bullets against the rioters to restore the calm.
The refugee center is located near the Turkish border and accommodates over 3,000 mostly Syrian and Afghan refugees.
Bulgaria lies on a part of the Balkan migrant route into Europe along which hundreds of thousands of migrants traveled in 2015. Some 1.8 million illegal border crossings were detected by the EU border agency Frontex in 2015.