He estimates that means up to 15,000 bags have not been screened by dogs, adding that this is a "ticking biosecurity time bomb".
"With the height of fruit fly and stink bug season approaching, this is embarrassing for O'Connor as his Government talked tough on biosecurity but have left farmers and growers livelihoods at risk."
A report, released earlier this year by the New Zealand Institute of Economic Research (NZIER), revealed an invasion of the brown marmorated stink bug could destroy more than $4 billion worth of fruit and vegetables.
Guy said the admission that the dogs aren't on duty while people are coming into the country during these times shows O'Connor "has been caught napping."
Speaking in the House yesterday, O'Connor said it would be "dishonest to say that it was a perfect system."
But he said the Government has put an additional $9 million into biosecurity, as well as bolstering its offshore intelligence unit.
"I think we run a far more robust system than was previously in place under the last Government."
But Guy is not blaming the dogs, rather what he calls a "toxic work culture" within the dog detector unit.
O'Connor admitted he is aware of claims being made about this type of culture.
"I received an email that has been passed on to the Director-General [of MPI]. I expect him to investigate those, and if any such culture exists, to get rid of it."