The Government only learned of new changes for meat exports into China when shipments were blocked from entering the country for the second time in two months.
On Thursday a shipment of New Zealand meat was prevented from entering Dalian, a major port in northern China.
The following day meat companies were told by officials at the Ministry of Primary Industries (MPI) to stop signing off export certificates until the issue was resolved, preventing meat being loaded for shipment.
Today Primary Industries Minister Nathan Guy and Food Safety Minister Nikki Kaye said officials would begin applying new export rules for meat into China from Monday.
The statement said it was made aware of the new rules on Thursday, when news of the blocked shipment emerged, despite the rules taking effect on June 1.
"In the last 48 hours we have sought clarity around the impacts of those requirements and officials have negotiated their implementation," the Ministers said in a statement.
Guy, who is in China leading a trade mission described the relationship between the two countries as "warm and professional", saying this allowed the issue to be resolved quickly.
The statement said the rule changes would have little practical effect.
For the 1323 consignments - around 30,000 tonnes of meat - sent since June 1, letters of assurance and scanned certificates will be sent by MPI officials in the coming days.
A quarter of the shipments would be delayed by "a couple of days".
The latest incident comes little over a month after a major block of meat exports into China was resolved.
In May, hundreds of tonnes of frozen sheep meat and beef was caught at Chinese ports for weeks, with the Government unable to explain what was causing the issue days after the block emerged.
Eventually the problem was blamed on a change of letterhead on export certificates, stemming from a departmental merger which saw the Food Safety Authority folded into MPI.
The issue was resolved when MPI began reissuing export certificates under the old FSA letterhead.