Alan Burnett, export manager for the Uddingston-based company, said some overseas customers’ lack of geographical knowledge was a factor.
“The further away you get from Scotland, the less most people know where it is. But the Japanese recognise the Union flag. We have definitely not rebranded.”
Tunnock’s, famous for its signature caramel logs, wafers, teacakes and snowballs, currently has a masive 40ft shipping container of its wafer creams on its way to Okinawa, due to arrive in September.
Further shipments are planned to leave in September and December.
Mr Burnett said since news of the Union flag emerged last week his company had been “inundated” with e-mails saying they would be boycotted.
He further added that the new packaging had been designed after the firm won orders for nearly two million biscuits.
Last year, the company attracted protests outside its factory in Uddingston, South Lanarkshire after marketing teacakes under the slogan “The Great British Teacake”.