Dozens of vacancies for civil service vets who carry out port and meat plant inspections remain unfilled, according to the trade union behind this week's strike action.
Nipsa general secretary Carmel Gates told The Irish News the staff shortages were a result of poor pay and higher salaries south of the border.
The trade union boss also claims that a significant proportion of Department of Agriculture, Environment and Rural Affairs' (Daera) staff are either acting up to higher grade positions or employed through agencies.
The department has not responded to the claims, which come as around 260 Nipsa members working in Daera's Veterinary Service Animal Health Group (VSAHG) begin five-day targeted strike action aimed at highlighting low pay.
The Nipsa members, along with a handful of counterparts from the GMB union, are due to strike at ports and meat plants from Monday to Friday, in a move that is expected to disrupt both checks on goods entering the north from Britain and the slaughter of livestock at a number of abattoirs.
Nipsa says the industrial action is on behalf of around 20,000 of its members in the regional civil service.
Ms Gates said five years ago the number of vacancies for vets was in "single figures" but that there were now up to 60 posts unfilled.
"Daera have been trying to recruit for these roles for some time but they are unable to find the staff and I believe it's down to the level of salaries on offer," she said.
The Nipsa general secretary said starting salaries for vets in the Republic were up £20,000 higher than those in the north.
"In common with all areas of the civil service, vets' pay levels need to addressed urgently or there will be a serious crisis – this strike is not just about pay, it's about the delivery of services too," she said.
The body representing large supermarkets has said it is concerned by the industrial action but said disruption to supplies would be minimal.
Director of the Northern Ireland Retail Consortium Neil Johnston said: "Consumers will notice very little impact on shop shelves in the short term as we are hopeful that movements through both red and green lanes of goods going into Northern Ireland will continue as normal.
"However, the possible significant impact of the strike on the agri food sector and the wider food supply chain is concerning."
Ms Gates said public sector workers had seen their living standards "crash".
"There is now a hard ‘pay border’ between workers in Northern Ireland and workers across the Irish Sea," she said.
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"I commend and thank these workers who are taking this action on behalf of their civil service colleagues but also on behalf of all public servants here – it is time for the secretary of state to listen to the ordinary people, meet with unions and direct senior civil servants to engage in meaningful negotiations to end this dispute."
SDLP MLA Patsy McGlone called for a "serious recruitment drive" from the department but argued that there would be fewer staff shortages if "staff received fair pay and working conditions commensurate with their role".
"The department has had ample time to prepare for this situation and they need to cast a wide net to get the people they need for these roles," he said.
