His tax agent had called the IRD which told her his GST cheque had been printed on inferior paper.
"It's the sort of thing you hear about in Monty Python," Mr Williams said.
IRD group manager, service delivery, Heather Daly, said 1240 refund cheques issued on November 3 were printed on incorrect paper.
"As the paper did not have the appropriate markings, banks were not able to accept the cheques."
The issue had been identified through a customer query, Mrs Daly said.
"The affected refund cheques were cancelled and we have been contacting customers and taking action to ensure they receive the payment, via direct credit or a new cheque, as soon as possible.
"We apologise to those affected for any delay and inconvenience. Immediate steps were taken to try to prevent any such error in future."
She would not reveal the total value of the dud cheques.