Burger King has been identified as one of the companies which regularly receives meat products from ABP/Silvercrest -- the company at the centre of the controversy.
The fast-food giant has reassured consumers that its burgers are not affected but has launched its own separate probe.
Silvercrest in Monaghan has decided to temporarily suspend production at its factory with immediate effect.
The move came after new test results found that nine out of a sample of 13 burgers showed the presence of horse DNA.
ABP/Silvercrest supplies Burger King in the UK but it also reassured consumers that the particular burger products supplied to the fast food outlets were not affected as they were on separate supply lines.
The meat product company emphasised that Burger King products have not been affected by the contamination.
"Whilst, we are temporarily closing down the entire plant for purposes of expediency, we would like to reiterate that all Burger King products produced by us are stored separately and manufactured on an independent line," it said. "There is no evidence of any contamination of raw material used for the manufacture of any Burger King products."
The company also said that it was confident that the burgers supplied to Irish and UK restaurants are not affected.
"The reported source of the raw materials contamination originated at two suppliers in Continental Europe," a statement said.
"Burger King restaurants in the UK and Ireland do not use beef from Continental Europe or from these suppliers.
"Burger King burgers in the UK and Ireland are made from 100pc British and Irish beef, with no fillers or other binders added and are made on a dedicated and separate production line."
However, the company added that it has embarked on its own investigation.
"Food quality is a top priority for Burger King Worldwide. As part of its comprehensive food quality programme, the company maintains stringent and overlapping controls and audits to oversee our suppliers," it said.
"As a standard precautionary measure, we have launched a complete investigation into this matter." A representative for rival burger chain McDonald's said its supply chain has been checked and it is not affected.
Minister for Agriculture Simon Coveney said they are making "good progress on the investigation" in identifying the source of the problem.
"I think the test results yesterday were helpful in those areas," he said. "It's not a big surprise that nine out of 13 burgers proved positive for some horse DNA elements yesterday."