It would not be illegal for people in the United Kingdom to join terrorist organisations such as al Qaida or Islamic State (IS) under the Green Party.
Natalie Bennett, the Greens' leader, said people should not be punished for what they think, but those inciting or committing acts of violence would feel the "full extent of the law".
The party would also reshape the military to create a smaller home defence force and progressively ease immigration controls.
Green Party policy states "it should not be a crime simply to belong to an organisation or have sympathy with its aims, though it should be a crime to aid and abet criminal acts or deliberately fund such acts".
On BBC1's Sunday Politics Ms Bennett was challenged about the policy and whether that would make it legal for people living in Britain to join brutal terrorist groups such as IS.
She said: "This is a part of our policy that I think dates back to the age of the ANC and apartheid South Africa."
Pressed on whether that meant it would be allowed to be a member of al Qaida or IS, she said: "Exactly. What we want to do is make sure we are not punishing people for what they think or what they believe.
"Obviously actions of inciting violence, supporting violence, those are absolutely unacceptable, illegal and should be pursued to the full extent of the law."
She added: "What we are talking about is a principle that you shouldn't be punished for what you think. And we need to balance, we do not protect freedom by destroying it."
Ms Bennett, who said she will represent her party in two televised leaders debates under the proposals set out by broadcasters, set out the Greens' views on defence, which include scrapping the Trident nuclear deterrent, leaving Nato and cutting the size of the armed forces.
"We obviously need to be able to defend our own borders, civil defence, and we have a real responsibility as a rich country to contribute to UN peacekeeping forces," she said.
Asked if that meant a home defence force, she said "yes" but would not give figures on how many personnel that would require.
On immigration policy, she said in the "medium term" the party's policy was to progressively reduce UK immigration controls.
She added: "What we want to do now is allow people who should have the right to be in the country, to be in the country. What we have to do is stop the race to the bottom on immigration rhetoric that we have been hearing, led by Ukip and sadly followed by the other (parties).
"People who should have a right to be here - which means asylum seekers and refugees - we are not treating them properly and we need to.
"British people who want to live with a foreign, non-EU spouse or partner here, on the Government's own figures 19,000 Britons can't live in their own country.
"We saw last year the number of foreign students applying to British universities going down.
"All of those are things that are causing real damage to people's lives."
Asked whether the party was committed to an "open doors" policy because it believed "richer regions do not have the right to use migration controls" she said the short-term policies would be those in the manifesto but added:
"In the longer term, thinking about 20, 30 years hence, we are talking about a different kind of society, a society in which the world is more equal, where it is more balanced."
Ms Bennett also defended the party's plan for a basic citizen's income of around £72 a week, paid to all people in the UK regardless of wealth or need.
She claimed "half the cost" of the £280 billion policy would be met by replacing benefits and reducing administration costs.
The plan would also remove the income tax personal allowance but Ms Bennett insisted: "No one on a low income will be worse off. I can say that very clearly and categorically."
She added it could mean that lower-paid "nasty jobs" could become harder to fill, requiring their wages to rise in order to attract applicants.
"Maybe we will have to pay sewer cleaners more than bankers, that might be a good thing," she said.
The money would give people a safety net if they wanted to try setting up their own business or work part-time, she said.
"What we want is for people to have a choice over how they live their life, to be able to build the kind of life they want."