Manitoba's chief veterinary officer says officials had no choice but to shoot 1,300 piglets to euthanize them last month.

Dr. Wayne Lees responded on Monday to concerns raised by a former employee of a hog farm near Austin, Man., that is the subject of an animal cruelty investigation.

His office ordered the piglets euthanized in late August, after investigators received a call about inappropriate treatment of animals at the farm.

Tony Heppner, who was working as a barn manager at the time, told CBC News the weanlings were rounded up into a pen and shot with a .22-calibre rifle.

"It's not pleasant. Nobody likes to do this. But we have to use the methods that are available and the facilities that are available," Lees said in an interview.

Investigators found the weanlings to be in "severe distress" and the animals were put down "to avoid further pain and suffering," the government has said.

Lees said he went to the farm last month and saw many of the piglets were starving, as they had been removed from their mothers and were not weaned.

But Heppner disputed the province's claim that the weanlings were in severe distress. The hog farm was under financial stress, but he said the piglets were being fed and cared for.

Some of the piglets were underweight because of a flu virus, he added.

Has nightmares

Heppner said officials had told him the piglets would be euthanized using a lethal injection to the heart.

"Some weanlings I watched get shot three, four times, five times … screaming," he said.

Heppner said he still has nightmares from watching the weanlings get shot, adding that some of the animals did not die quickly.

"I didn't eat for a day and a half, two days … I couldn't sleep," he said.

Bill McDonald, chief executive officer of the Winnipeg Humane Society, said shooting piglets several times, all at once and in the same space, is not humane.

"It's got to be up close and personal — it's a single head shot, and the animal's restrained, and it's done very, very quickly," McDonald said.

"If this report is accurate and someone was standing [and] shooting four or five times, that's not good."

Lethal injection wasn't an option

McDonald said the province should have separated the piglets and euthanized them individually.

"We, and any shelter in North America, would recommend euthanasia by lethal injection," he added.

Lees said shooting the pigs is an acceptable method of euthanizing animals, but he admitted that some of the weanlings had to be shot more than once.

"There are no practical ways of giving injections to that many animals. I don't know how you would give intravenous injections to 1,300 animals," he said.

Lees said work is being done on a prototype for gassing large numbers of animals, but he added that the project is only in the development stage.

The hog farm has been owned by HP Farm Equipment in Winkler but it was managed by two brothers, Bernie and Menno Bergen.

The owner of HP Farm Equipment had told CBC News that the brothers were in arrears to him for several years and were in financial distress.