The department store group booked an exceptional £47.3m charge after discovering an error in the way it had calculated pay for Sundays and bank holidays.
Excluding exceptional items, pre-tax profits for Waitrose and John Lewis rose 3.9 per cent to £115.8m.
“The partnership has had a strong first half ... slightly ahead of our expectations due to a good trading performance in both businesses,” chairman Charlie Mayfield said.
“Despite a strong second half last year, both during the Olympics and at Christmas, I expect us to trade positively in the second half.”
Like-for-like sales were up 6.9 per cent at the upmarket Waitrose supermarket chain while like-for-like sales were up 5.1 per cent at the John Lewis department store.