The fast food chain, with more than 500 outlets in Ireland and the UK, said food quality and safety were "a top priority".
"While this is not a food safety issue according to findings from the Food Safety Authority of Ireland (FSAI), on learning of these allegations, we immediately launched an independent investigation that is ongoing.
"As a precaution, we decided to replace all Silvercrest products in the UK and Ireland with products from another approved supplier."
Silvercrest, a subsidiary of Larry Goodman's ABP Food Group, last week suspended its operations in Co Monaghan after traces of horse DNA were found in samples of its burgers. It destroyed more than 10 million burgers.
It was previously indicated that the source of the contaminated material was a third-party EU supplier, but new information has cast doubt on this.
Fianna Fail agriculture spokesman Eamon O Cuiv said: "He [Mr Coveney] indicated very strongly that the source of the product was from abroad.
"But in his answer yesterday in the Dail, he made it clear they are not now certain about that."
The Burger King decision showed the need for more urgency from Mr Coveney and his department.
"The future of our successful and highly lucrative beef industry is being jeopardised by a lack of information," he added.
Communications Minister Pat Rabbitte said Mr Coveney had been "scrupulous" about putting all the information he has into the public domain.
Mr Rabbitte said Burger King had to switch supplier as the Silvercrest plant had closed temporarily.
The controversy was sparked by results of tests by the FSAI showing frozen burgers made by Silvercrest had horse DNA of up to 29pc relative to beef content.
The Department of Agriculture has yet to comment on Burger King's move, which was reportedly influenced by the slow pace of the official investigation into the scandal.
It is believed there was concern within the fast food giant over a lack of communication from the Department of Agriculture.
While precise figures are not available, it is estimated the Burger King contract with Silvercrest is worth around €30m.
ABP said it would not be commenting further pending the conclusion of its internal investigations.
Food marketing organisation Bord Bia said the Burger King decision was "an inevitable short-term consequence of the temporary closure" of the Silvercrest plant.