Hundreds of protesters gathered in Portsmouth after a boat carrying about 140 migrants was brought ashore in Hampshire.
Demonstrators blocked roads in an attempt to stop coaches carrying the migrants from leaving the city on Sunday night, following a separate protest at the Port of Dover the previous day.
Hampshire Police said a small number of officers were injured and vehicles were damaged, with an investigation now under way to identify those responsible.
The government said people had a right to peaceful protest but condemned "intimidating and thuggish behaviour" at the demonstration.