The effective tax rate for the pharmaceutical industry appears ready to go higher thanks to a changing business model and governments that are looking to get tough on corporations that shelter their taxes, according to a new study from PricewaterhouseCoopers.

A sample of a a dozen global drugmakers found that, between 2001 and 2006, the average tax rate was just 23.8 percent - at the high end, Bayer’s rate was 29.3 percent and Novartis had the lowest at 14.4 percent. Among biotechs, Cephalon clocked in at 39.9 percent.

Most drugmakers aren’t surprised to hear the bad news. Six of 10 senior pharma tax execs told PwC they see an increase in the effective tax rate as inevitable. Of course, the recession is making goverments eager to find new revenue and restrict tax havens. In particular, authorities will look for abuses of intra-company transfers of expenses or profits (here’s a link to the report).

And the shift to a more service-orientated business model is likely to have serious implications. PwC notes that, as personalized medicine becomes more important, drugmakers will package meds alongside services such as diagnostics and patient compliance monitoring. “Pharmaceutical and life sciences companies could not only face new and higher taxes as a service provider but they will have less ability to allocate profits to lower tax rate locations,” PwC writes.

How to minimize the tax bill? PwC suggests several things, including expanding the function of regional hubs in places where generous R&D tax incentives are offered. Another consideration is how acquistions should be financed - traditional debt financing may take a back seat as pharma deals with entities that have different tax structures, such non-profits and venture funds. Meanwhile, Asian countries are offering aggressive incentives - low rates, for instance - to establish facilities.