Inland Revenue says it kept a recent outbreak of the Win32.Sobig.C virus on its systems under control, but a website designer has criticised the department for "slack security".
An IRD statement says the department's main tax systems "have not been impacted" and that "on identification of the virus, IRD ceased all email operations and began an eradication process".
It has listed steps on how to deal with the virus here.
Internet commentator Bruce Simpson raised the virus issue on his website yesterday, after being contacted by people who received email sent by IRD computers.
Website designer Tom Scott says he received 20 emails from the IRD transmitting the virus.
"I'm a little disappointed at the IRD for having such slack security and that they couldn't keep their antivirus software up-to-date.
"They have some of the most sensitive information in the country and I'd like to know how such a thing could happen.
"It's just not good enough to say 'sorry' and expect us all to roll over and accept that as a final offer.
"Luckily nothing came through to my network as I use Mailwasher to filter out spam."