The discount fashion chain said it had come to its attention that the footwear "does not meet the Primark usual high standards for chemical compliance".
The products in question are men's flip-flops in blue, black and khaki.
The company said customers will be offered a full refund and do not have to produce proof of purchase.
Primark, which is owned by Associated British Foods, said the footwear was sold in stores between 4 January and 2 June this year as part of its Cedar Wood State range.
"We have found levels of a restricted substance in the product in excess of the 1.0 mg/kg requirement," it said on the website.
A Primark spokesperson confirmed that the chemical in question was chrysene, used in dark coloured dyes, but said it was present at levels that would pose a minimal health and safety risk to customers.
The fault was discovered by Primark following up an inquiry by a third party, the company said.
"We take the safety of our customers, and the quality of our products very seriously," the spokesperson said.
The company has suspended all new orders from the factory that manufactures the flip-flops while the matter is investigated.
Primark has recalled thousands of men's flip-flops over fears they may contain dangerous levels of a cancer-causing chemical.