Leading environment protection agency Forest and Bird says habitat that has missed out on pest control in the past year is now worse off than before.
The Department of Conservation's latest annual report shows it failed to meet targets on possum, goat and weed control in 2013 due to a staff shortage.
Forest and Bird Campaigns and advocacy manager Kevin Hackwell said the pest control work would have to be made up, but the odds were it may never be made up at all - and that was a real problem for native animals and plants living in those sites.
Mr Hackwell said DoC needed to be funded adequately to protect the country's diversity.
He said restructures had been awful for the department and have led to staff being slashed on the front line.
But DoC director-general Lou Sanson said his department can do its job and staff were still feeling the impact of the last restructure.
He said the restructure was emotionally hard on staff and the nature of some of their roles changed.
"They had to apply for jobs, some people were demoted, some people lost seniority, the regions were bigger, there was more travel."
However, Mr Sanson believed the department needed a change.
"The staff have worked incredibly hard over the past year and turned the organisation around," he said.