Mr McDonnell said he “wholeheartedly” agreed with his fellow retailers in concerns over the tax raid.
He added: “The bill for the retail industry is around £7bn so all of us concerned are looking at multi-million pound bills.”
Mr McDonnell was among the 80 senior industry leaders who signed a letter to the Chancellor over the weekend, arguing they could be forced to raise prices for shoppers as a consequence of the changes.
Lidl said it would continue to have lower prices than its rival supermarkets, although Mr McDonnell did not rule out increases.
He said: “It would be remiss of me not to say there has to be inflationary pressure.”
The comments came as Lidl said it swung back into a profit last year after it gained more than 300,000 new shoppers over the year.