Russel Norman has pleaded guilty to interfering with an oil survey ship in April last year.
The former Green Party leader did not seek diversion when it was offered, instead hoping for a discharge without conviction "on the basis [his] conduct was justified and necessary to bring about required change to Government policy", according to Greenpeace.
The Ministry of Business, Innovation and Employment last week indicated it would drop the charges against Greenpeace, of which Dr Norman is executive director, if the pair pleaded guilty. Greenpeace had faced fines of up to $200,000.
Climate activist Sara Howell also pleaded guilty, hoping for the same outcome as Dr Norman. Sentencing for the pair will happen in July.
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In April last year they protested the presence of the Amazon Warrior, which was exploring for oil 50 nautical miles off the coast of Wairarapa, by jumping into the water.
They were the first to be charged under an amendment to the Crown Minerals Amendment Act made by then Energy Minister Simon Bridges. The offence carries a potential penalty for an individual of one year in jail or a fine of up to $50,000.
Initially they pleaded not guilty.
"To paraphrase the late, great Tom Petty, we won't back down, we will stand our ground," Dr Norman said in October when they were charged. "The future of humanity is at stake in this climate battle against the oil industry and their Government."
On Friday they said the "best course of action now is to plead guilty while making a plea in mitigation in Court on the grounds that our actions were reasonable and honourable given the threat of climate change".
"Taking this route will also save supporter money and court time, and allow us to continue tackling climate change," Dr Norman said.
A third person involved in the protest, Gavin Mulvay, accepted the offer of diversion in October.
In the time since the charges were laid, the National-led Government has been replaced by the Labour-NZ First coalition with support from the Green Party, which outlawed most future offshore oil and gas exploration.