Live-streamed footage of sheep having their throats cut at a Napier meatworks did not constitute animal cruelty, the factory owner says.

The footage was streamed on Facebook last week by Fresh Meats NZ employee Te Amorangi Kireka-Whaanga, a prominent one-time Isis (Islamic State) supporter.

In a video he posted to Facebook last week, a man is seen laughing as a thrashing sheep is held down and its throat cut. Animal welfare group SAFE said the fact the sheep was moving suggested it was still conscious when it was slaughtered.

But after watching the footage, meatworks owner Fresh Meats NZ said claims the video showed cruelty to animals were untrue, and the slaughter complied with New Zealand's strict halal and animal welfare protocols.

The company said animal welfare was "at the forefront" of all its work and it did not tolerate animal cruelty.

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The worker has been accredited by the Federation of Islamic Authorities NZ, Fresh Meats said.

"External verification by [the Ministry for Primary Industries] as well as internal verification by our quality assurance team confirm that our humane slaughter and animal welfare processes are acceptable," the company said.

Kireka-Whaanga has in the past voiced his support for the terror group Isis.

Fresh Meats NZ says it is aware of those allegations but that Kireka-Whaanga has denied them.

However it says it will conduct an investigation and consult with authorities.

"Fresh Meats NZ regards the safety and security of all our employees as paramount."