A milk products company which announced it would ditch its Halal certification after it was targeted on social media has now reinstated it and won back a deal to supply Emirates Airlines.

The Fleurieu Milk and Yoghurt Company, south of Adelaide, found itself the target of a coordinated global anti-Halal campaign late last year and rejected suggestions the fee it was paying was being used to help fund terrorism.

Without its certificate, the company could not fulfil a $50,000 contract to supply yoghurt to Emirates.

To achieve Halal status, the company needed to ensure no pork, blood or alcohol got anywhere near the production process.

Fleurieu Milk Company executive Nick Hutchinson said it had now changed its mind, reinstated its Halal certificate and ensured the airline contract was secure.

"We should have stayed tight, made a stand for Australia as a country that accepts and appreciates different ways of life," he said.

"I know full well that there will be a lot of people out there that are extremely disappointed with our decision and will be quite vocal about it, but for us we think we've done the right thing."

Mr Hutchinson said he felt the company was sending the wrong message by ruling out a religious group from being able to enjoy its produces.

"We have now gone back on that and we have regained halal certification and are quite proud to say that anybody of any sex, age, race, religion as well is able to enjoy our products," he said.

The Islamic Society of South Australia, which provides companies with certification, said the attacks against Halal products amounted to "Islamophobia".

A Senate inquiry into food certification schemes has just been set up by SA Liberal senator Cory Bernardi, with backing from his party colleagues and six Upper House crossbenchers.

Senator Bernardi said he wanted to examine the claims made on social media by the Halal boycotters, and Mr Hutchinson said that parliamentary investigation would be a welcome move.

"The Senate inquiry, they're probably in a similar position to us, they just want to get answers and put it to bed," he said.