"Cadbury has voluntarily removed two of its products from the shelves," the minister told AFP.
The tests were conducted by the ministry which over the weekend announced that two Cadbury products contained pork traces.
Chocolate products are popular in Malaysia and can be found in most shops nationwide.
Pork and its by-products, alcohol and animals not slaughtered according to Islamic procedures are not considered halal(permissible) and are forbidden to Muslims.
Cadbury Malaysia, a part of the British multinational owned by Mondelez International, said it was withdrawing the Cadbury Dairy Milk hazelnut and Cadbury Dairy Milk roast almond products.
"Ensuring that all our products made here in Malaysia are halal is something we take very seriously," it said in a Facebook posting.
Meanwhile anger among Muslims is mounting, with one senior religious official calling for a hefty fine or a shutdown of the Malaysian plant.
Syaikh Ismail Muhammad, the grand imam of the national mosque in Kuala Lumpur, was quoted by Bernama news agency as saying tough action would serve as a lesson to other food producers to ensure their products were halal.
Subramaniam said Cadbury was working with Islamic religious authorities by sharing samples to test for non-halal ingredients.
"We want to know how the product became contaminated with pig DNA. The health ministry will also do additional tests," he said.
Cadbury is the world's second largest confectionery brand after Wrigley's.