One of South Australia's biggest takeaway coffee retailers has banned serving coffee in reusable cups and mugs — including its own branded containers — at more than 130 stores across the state.

In a document circulated among its staff, service station On The Run states the policy was introduced for safety reasons, citing the risk of contamination posed by refillable containers.

Key points: Service station chain On The Run says dirty containers present a safety risk to customers

Service station chain On The Run says dirty containers present a safety risk to customers On The Run said it was committed to a "better solution"

On The Run said it was committed to a "better solution" More than 1 billion disposable coffee cups end up as litter or landfill each year

But the ban has angered some consumers and an environmental advocate, who said it went against the trend towards responsible consumption.

"Other service stations and coffee shops have been going out of their way to encourage people to bring in their own reusable cups or they're providing them with ceramic cups," said Jon Dee, founder of advocacy group DoSomething.

"On The Run really has made a major mistake and I think they're underestimating how angry South Australians will be about this.

"South Australia is the state that is known for doing the right thing by the environment.

"As we saw with the War on Waste TV series with Craig Reucassel, Australians are using over a billion disposal coffee cups every single year, and most of those are ending up as litter or in landfill."

Last year, the Adelaide City Council offered coffee shops and cafes a rebate to encourage customers to bring their own cups to prevent waste.

On The Run said its policy was introduced for safety reasons and intended to protect consumers. ( Supplied )

On The Run is continuing to serve coffee in its disposable cups, and explained its policy was intended to protect customers by preventing the spread of germs.

"We cannot control contaminants (bacteria, mould, viruses, foreign objects, etc)," the company memo stated.

"Foreign containers present a high risk of cross-contamination when they come into contact with food preparation areas and equipment."

Dirty cups cited as reason for policy change

In a statement, an On The Run spokesperson said the company would have preferred to continue serving coffee in reusable cups and mugs.

With more than 130 outlets, On The Run is one of SA's biggest sellers of takeaway coffee. ( Google )

"We have had many incidents of customers bringing in dirty, unhygienic, contaminated cups," the spokesperson said.

"More recently we had an incident where a customer brought a cup in that was contaminated with a heavy metal."

SA Health has confirmed it has no policy on reusable coffee cups.

On The Run sells disposable containers under its C Coffee brand, and Mr Dee said the ban raised the issue of refunds.

"The really disappointing thing here is that On The Run have actually been selling refillable coffee cups to their customers and they're now telling them they can no longer use them," Mr Dee said.

"Are they giving the money back to people who in good faith bought those refillable coffee cups?"

The company said it was "heartening" that "so many people feel strongly about this" and has committed to investigating "better solutions".

"We realised that there are other more common potential health risks in us serving coffee into cups that we can't guarantee are clean and ready to use," the spokesperson said.

"Some people are particularly sensitive to this kind of risk, and they are our customers too. It is difficult for us to accommodate washing cups."