Last year the company replaced plastic straws with paper ones across all of its UK and Ireland restaurants after a successful trial period.
According to an internal memo, the new paper straws are not recyclable and must be binned or burned, The Sun newspaper has reported.
"While the materials are recyclable, their current thickness makes it difficult for them to be processed by our waste solution providers, who also help us recycle our paper cups," the spokesman added.
"We are working with them to find a solution, and so the advice to put paper straws in general waste is therefore temporary.
"This waste from our restaurants does not go to landfill but is used to generate energy."
The move to paper straws came amid growing pressure on companies to reduce single-use plastic products and packaging.
It followed mounting concerns over plastic pollution in the oceans where items such as straws end up harming wildlife such as turtles and fish.
When it confirmed the move, McDonald's said the two suppliers it had found to meet its needs for paper straws were the start-up Transcend Packaging based in Wales, and global company Huhtamaki which would produce the straws at its plant in Belfast.
The fast food giant also said that its plastic straws at the time were made from "100% recyclable material".
The spokesman for McDonald's said the company uses 1.8 million straws a day and that the move to paper was a "significant step in helping reduce single-plastic use".
"We are working hard to boost training and education in our restaurants to increase our recycling rates, and also encourage customers to recycle," he added.
"Over the past few years, the number of items we recycle has increased in line with our volume growth, in particular we have seen an increase in cups recycled - with 40 million recycled last year, however we recognise this is something we need to continue to focus on."