Saboteurs have destroyed genetically modified potatoes in the Crop and Food Research complex near Christchurch.
The cost of the attack is expected to be more than $100,000, with research set back by months.
One of the projects worst hit was looking into better ways of non-GM potato improvement.
The crown research institute's "contained laboratory" for GM experiments at the Lincoln Agriculture and Science Centre, a big glasshouse, was broken into early yesterday. The green tops were cut from plants and pots were emptied into rubbish bags.
Crop and Food chief executive Paul Tocker said 1334 plants from three research projects were damaged, with the cost exceeding $100,000.
"These are not field trials," Mr Tocker said.
"It is breaking and entering a science laboratory with the intent to disrupt the progress of science."
Crop and Food's GM potato work was attacked in 1999 in one of the first high-profile protests in New Zealand.
Last year, after the Government decided not to extend a moratorium on GM field trials, the Wild Greens group said protesters were focusing on 10 areas where trials might occur.
It said more than 3000 people had put their names to a pledge to take direct protest action.
Mr Tocker said the latest raid had severely affected work by Dr Margy Gilpin, whose project was trying to identify genetic sequences linked to specific traits so conventional selective breeding of the plants could be improved.
Dr Gilpin said she was devastated by the damage. "Ironically, our programme is studying genetic techniques to help us find better ways of non-GM potato improvement."
"Because the plants have now been either destroyed or cannot be accurately identified, we will be unable to do the tests to verify all the science progress we have made over the last three years."
Mr Tocker said the sabotage had hit two other GM and non-GM research programmes, including work on improving pest and disease resistance to minimise the need for chemicals.
He said the destruction was a senseless waste.
The institute would boost its security precautions.
Constable Rob Stuart of Lincoln said a previous break-in gave investigators obvious leads to follow.
"There probably will be several people that will be spoken to, but that is later down the track," Constable Stuart said.
He said security at the centre was good after being upgraded following the first break-in.
Environment Minister Marian Hobbs said yesterday's attack was particularly stupid because the trial was contained in a laboratory.
"This is a bit like someone opposed to nuclear weapons attacking a nuclear power station. It's a very confused piece of action."
Ms Hobbs said the destruction of the plants was "intellectual theft".
The chairman of the pro-GM group Life Science Network, Dr William Rolleston, said the destruction of the plants was an attack on knowledge.
"This was not a field trial. It was in a contained laboratory, which is something I thought no one was opposed to, so it's strange."