Searches were also carried out at different locations across Northern Ireland on Wednesday.
More than 120 HMRC officers took part in the raids at 16 premises with the arrests of two men and a woman taking place in Newry
The two men were aged 49 and 47, while the woman was aged 37.
All three have been released on bail.
Computers and business records were seized during the operation.
Business premises were searched in Newry; Belfast, Newtownabbey, Antrim, Derry/Londonderry, Armagh; and Dungannon areas.
Assistant director of HMRC’s fraud investigation service Steve Tracey said: “Tax fraud is often thought victimless but it isn’t; the public lose out on vital funds for essential services. We will continue to work with our partners to tackle this crime.”
Anyone with information on tax fraud is asked to contact HMRC online or to contact its fraud hotline on 0800 788 887.