Some food producers are "flouting" new guidelines on social distancing and not providing personal protective equipment, a union claimed.
Unite said workers across Northern Ireland had been left "hugely confused" by the Prime Minister's Covid-19 restrictions.
Food manufacturing has been under unprecedented pressure as supermarkets are stripped of product.
Industry representative group Manufacturing NI has said factories choosing to keep going should "directly or indirectly support life-sustaining and necessary parts of the economy".
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Susan Fitzgerald, regional coordinating officer for Unite, said: "Across the front-line production sector - in particular in food - workers are reporting widespread management flouting of guidelines on social distancing and the lack of personal protection equipment.
"In some cases when workers go into self-isolation with symptoms or even test positive for coronavirus, bosses are refusing to shut down their working area or conduct a deep-cleanse, and expect their colleagues to continue in work instead of self-isolating.
"Indeed, some workers have informed Unite that employers have written to their workers to tell them they cannot be held liable if they contract coronavirus at work."
Manufacturers have had to react quickly over recent days as the virus' spread has intensified.
On Monday, Boris Johnson said people must remain at home except for shopping for basic necessities, exercise, any medical need and travelling to and from essential work.
Shops selling non-essential items were told to shut and gatherings in public of more than two people who do not live together are banned.
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Manufacturing NI said: "To help understand if businesses should stay open, we are asking to ask themselves:
"Does what you do (or some part/people within your business) directly or indirectly support life-sustaining and necessary parts of the economy and our public services? If the answer is yes, then you could choose to keep going. If the answer is no, then the Government expect you to close.
"Can you do it safely with 100% compliance with hygiene and distancing advice? If the answer is yes, then you could choose to keep going. If the answer is no, they expect you to close.
"There is currently no list of essential services or functions available, but we are asking for this and will share when received.
"Anyone who does not need to be at your factory should be at home."
