Opponents have leapt on the diverging views as further evidence of the disintegration of the party, which will not have any current MPs in the next parliamentary term and has been plagued by caucus in-fighting and a leadership coup.
Labour's Epsom candidate David Parker put up a sign across his billboards in the electorate: "Vote Banks - Get Both Dopes!"
"This is a circus," Mr Parker said.
"Mr Banks is anti-abortion, anti-gay and now he's tied up with someone who is pro-decriminalisation of marijuana."
Mr Banks, who was not told of the marijuana announcement beforehand, said a softer stance on cannabis would not be party policy.
When asked if he alone made those decisions, he said: "No, but I'm telling you, the decriminalisation of marijuana is not going to happen.
"I'm in no awkward position. I've had people [in Epsom] asking me [about Dr Brash's speech]. It's his personal view, not a party view. It's not [party] policy, and it won't be.
"We need a public conversation around all of this. What we don't need - and I respect other people's view, including the leader of the Act Party - is to send out a message that we're going to go soft on marijuana."
Dr Brash is in lonely political territory; both National and Labour oppose decriminalisation of cannabis.
He said he would like the party to adopt his stance as its policy, but did not expect that to happen given that the board had set up a law and order sub-committee, chaired by Mr Banks.
He said it was not antagonistic to have the opposite view to the person he is relying on, given current polling, for his ticket back to Parliament.
"It's different. I accept that. We are close friends and I respect his judgement. We don't agree on this particular issue. We agree on virtually everything else."
He said it was an important debate, given the vast amount of police resources that appear to be having no impact on consumption.
Prime Minister John Key shrugged off suggestions that Act was imploding, and said National would continue to pursue mainly the party vote in Epsom.
Act candidate Don Nicholson said he did not have a view on marijuana, but he agreed with Dr Brash that current policy was not working.