She said it needed to be reviewed, as she was asked about what her party would do to increase security.
Prevent was set up by Labour in 2003 and its remit was widened by the Conservative-Lib Dem coalition in 2011.
Home Secretary Amber Rudd recently said if the Conservatives were re-elected, the strategy would receive more money.
Setting out her views on Prevent on the Andrew Marr Show, Ms Lucas said: "Many in the Muslim community believe it's been an attack on their group in particular.
"We absolutely want there to be a mechanism whereby people can come to the state with concerns, but when it is perceived by the Muslim community itself as being a toxic Big Brother brand, then we need to look at it again."
Prevent is designed to support people at risk of joining extremist groups and carrying out terrorist activities, focusing on schools, faith organisations, prisons and other communities where people can be at risk of radicalisation.
Ms Lucas also defended her opposition to mass online surveillance, saying the security services should focus on "targeted" measures.
The Green co-leader told Andrew Marr she and colleague Baroness Jones had been labelled "domestic extremists" in the past by police because of their campaigning and protesting activities, which was, she said, a waste of officers' time and resources.
Green Party co-leader Caroline Lucas has called the Prevent counter-terrorism scheme "toxic", saying Muslim communities feel "attacked".