Yvette Cooper has said that some supporters of Palestine Action "don't know the full nature" of the group, following the mass arrest of more than 500 people at the weekend.
Defending the organisation's proscription, she stressed it was "not a non-violent organisation".
The home secretary said tens of thousands protested lawfully about the "horrendous events" in Gaza without involving Palestine Action, which was banned under terror legislation last month.
Palestine Action won permission to challenge the ban, with a hearing set for November, and Amnesty International described the arrests as "deeply concerning".
The proscription made membership of or support for Palestine Action a criminal offence, punishable by up to 14 years in prison, and happened after followers caused an estimated £7m of damage to jets at RAF Brize Norton.
