The AIBP meat factory in Bandon, Co Cork, had its licence to slaughter suspended for four days last Friday.
The suspension followed the killing of a cow suspected of having BSE, after a Department of Agriculture vet deemed it to have failed a visual test.
The incident happened when a Department veterinary inspector at the plant, which services all of west Cork, ordered that a cow which was about to be killed be removed from the line.
He was concerned that the cow appeared to be very nervous. This is one of the symptoms displayed by animals suffering from bovine spongiform encephalopathy.
However, later last Friday he discovered that the animal had been slaughtered with a group of 20 others which had been on the line at that time.
According to the Department, the inspector immediately ordered a shutdown of the killing line until a full investigation of the incident was carried out under strict new EU regulations.
The Department said the carcass of the animal and the specified risk material - offal from the 20 other animals killed at the same time - were sent for destruction and rendering to the special plant designated for this purpose in Co Cavan. None of the meat from the animals entered the food chain.
The suspension of the licence at the plant, which kills up to 500 animals a day when in peak production, was lifted on Wednesday when the Department was satisfied that new arrangements had been put in place so a similar incident could not recur.
A Department spokesman said the company had told its investigators that a review of the animal holding arrangements at the plant had been carried out to prevent a repeat of the incident.
He said the farmer who sold the cow for slaughter had told the inspector that the animal had fallen when it was leaving the trailer, and this accounted for its nervous state.
The head of the suspect animal has been sent to the Department's laboratory in Dublin to test for BSE, and the rest of the farmer's herd is being monitored for symptoms of the disease.
A spokesman for the company confirmed that a notice to suspend killing under Section 12 (7) of the European Commission's Fresh Meat Regulations, 1997, had been served on the company last Friday.
"Our primary concern is public safety and animal and public health, and the matter has been investigated and the plant is now in full operation again," he said.
Company sources said production at the plant had not been seriously disrupted because no killing had been planned for Monday or Tuesday, when the company was told it could reopen again.