Tension heats up between Puntland and Somaliland
Television footage showed police wielding clubs and beating the migrants as they jumped from a balcony, while local residents in the side street hurled stones at them as they tried to run away.
Closer to Africa than the Italian mainland, Lampedusa has been overwhelmed by thousands of Tunisians fleeing unrest from the social upheaval at home.
More than 48,000 have reached the shores of southern Italy since the start of the year.
Many of the 1,200 migrants held in the centre fled when three fires broke out late on Tuesday.
The fires were allegedly lit deliberately by Tunisians protesting against their imminent return home, having been ruled to be economic migrants rather than bona fide asylum seekers.
The two regional states have been at loggerheads over the control of the Sool and Sanaag regions which are located on their border.