Council leader Steve Pitt said the decision had caused “needless disruption”.
Around 200 people, some wearing masks, confronted police in riot gear after they descended on the Eastney Landing ferry port area, where the migrants were landed.
Police protected a number of coaches parked on a road leading away from Eastney Marina as protesters blocked traffic. A dispersal order was put in place, meaning anyone failing to comply with police could be arrested.
In a statement, Hampshire and Isle of Wight Constabulary said a handful of officers were treated at the scene for injuries, none of which were serious.
It said: “Violence and criminal damage have no part in peaceful protest.
“No arrests have been made at this time, however an investigation to identify offenders responsible for any assaults to officers, criminal damage to vehicles or other criminal offences has been launched.”
Spencer Wragg, chair of Hampshire Police Federation, said: “I’ve seen footage of officers being pushed off their motorbikes, I’ve seen pictures of police vehicles damaged. It appears that the police last night became the target for some of the protest.”
Daniel Thomas, known as Danny Tommo – an associate of far-right activist Tommy Robinson – was livestreaming from the scene – where he called for his supporters to “get down to Eastney” and stop the migrants being transported.
The coaches carrying the migrants were able to leave in the early hours of Monday and the Border Force confirmed “individuals from the boat have been transported outside of Hampshire for processing”.