The error concerns most paperwork concerning same-sex married couples, although couples ordering personal ID papers (personbevis) from the office should find they are accorded the correct status.
The Swedish Tax Agency blames the problem on the fact that the law came into effect with little warning. Officials said the necessary changes to their computer systems would not be in place until November.
Sören Juvas, chairman of gay rights group RFSL, criticised the tax office's tardiness:
"I think it's taking too long to carry out these changes," he told Sveriges Radio.