Borders head of supply chain Geoff O'Neill said: 'There have been a few minor issues with Harper Collins deliveries of late but nothing significant.
'Borders has worked closely with Harper Collins over the past few months to plan our stock flows for Christmas. The execution of this plan is going as expected and these issues have not impacted our plans for an excellent Christmas.'
HarperCollins said it was business as usual and they were confident of fulfilling all orders. It has been trialling a distribution system at the depot since January, but only implemented it formally a few weeks ago.
A Waterstones' spokeswoman said the company was continually working with all its suppliers in the run-up to Christmas to ensure trading goes smoothly.