The Ministry for Primary Industries admits it needs to spend time finding out why lower biosecurity risk items are being missed at airport checkpoints.
A survey of 8000 passengers was carried out in Auckland, Wellington and Christchurch to measure compliance with biosecurity legislation.
It found the overall compliance rate was 95%, which is 3% below the Government's target.
Ministry spokesperson Roger Smith says the shortfall was mostly due to low risk items such as dirty shoes.
"We can improve looking for those goods, but for the high risk and medium risk goods we're very comfortable and very satisfied."
He says some weaknesses were identified and as a result the ministry will be making sure their staff have the appropriate training and that people are in the right place at the right time.
Mr Smith says there will be a point where the risk is so low it doesn't need to be addressed.
"We don't want to spend a lot of our energy and resources looking at items that are very, very low risk."