The legislation now covers 59 pages compared to the original plans that only ran to 25 pages, the CIOT said.
The draft legislation was first published in December 2010. At the time there were concerns that many ordinary commercial arrangements that have no tax avoidance motive would potentially remain within the scope of the rules and that this would add to the administrative burden and the absolute tax cost for larger UK businesses.
The legislation has now been amended and updated. It includes 14 separate tax avoidance tests governing when and how a set of exclusions will apply. But this, in the view of the CIOT, leaves the exclusions "intricate and heavily qualified".
Colin Ben-Nathan, chairman of the CIOT's employment taxes sub-committee said: "We think that employers will face real difficulties in trying to assess how they stand with this new legislation and that they are likely to need to take advice to arrive at a considered view.
"Even then that does not necessarily mean that HMRC will agree with the view that has been taken, leaving employers open to potential uncertainty on whether or not tax charges arise and at what point. We suspect many employers will want to seek clearance from HMRC on their particular arrangements and we wonder whether HMRC has the resources to cope and what the turnaround time will be.