Biosecurity New Zealand has revoked Plant and Food Resarch's approval to carry out field trials of genetically modified brassicas near Lincoln and tightened conditions relating to the trials.
The trials were halted earlier this year after it was discovered that the crown research institute was breaching its operating conditions by allowing a GM brassica plant to flower in the open environment at the site.
A report by Plant and Food Research into the incident released on Tuesday recommended shutting down the trials.
Biosecurity New Zealand says cross-pollination is unlikely to have occurred between the GM crops and those on properties surrounding the research site.
It has issued some interim measures in response to the report, including increasing the audit regime for the field trials, more effective internal monitoring and more staff training to ensure proper understanding of field trial requirements under the Hazardous Substances and New Organisms Act.
The agency's operational standards manager Clive Gower-Collins says Biosecurity New Zealand has conducted its own separate investigations and found it was highly unlikely that genetically modified pollen will have cross-pollinated with other crops.
Soil and Health Association spokesperson Steffan Browning, who alerted Plant and Food to the flowering GM brassica last year, said crop testing needs to be carried out to ensure no cross-contamination has occurred.
Mr Browning says none of the neighbouring properties should have to meet the costs of carrying out such tests.
In its report, Plant and Food Research recommended its trial be closed down and the site monitored for a year to ensure no new genetically modified plants grow back.
The incident report concludes there was a serious error of judgment by the trial's manager not to follow correct procedures by digging out the plant's stem and roots to prevent re-growth after harvest.
That led to serious non-compliance of the trial's consent conditions.
The crown institute's report said a relatively limited resourcing of the project led to time pressure being put on the trial manager at the time of harvest.
Plant and Food has another field trial into GE onions that was due to start last month, but that has been put on hold while investigations into the brassica trial are carried out.
GE Free New Zealand and the Soil and Health Association say closing the trial is a good move, but say Plant and Food should lose all its permits to carry out genetic modification trials.
Research into genetically modified plants must follow strict criteria set by the Environmental Risk Management Authority, including a requirement to prevent flowering and pollen release from the plants.