Concerns among corporations are so intense that advisers are seeing a pick-up in inquiries about moving corporate headquarters out of the U.S., she says. Arnold adds that companies are looking not at tax havens like Bermuda, but at Canada and the U.K, because "their tax plans with regard to earnings earned outside their regime are to many companies more rational."

Hank Gutman, a tax principal at KPMG, notes that the administration could refine its tax proposal when it releases its next budget. Companies should be watching to see whether the administration offers to lower the corporate tax rate in exchange for eliminating some loopholes, Gutman says.

He notes the proposed tax changes are only expected to raise $160 billion over 10 years, a drop in the bucket given that the federal deficit is projected to top $10 trillion. Gutman predicts the mammoth deficit will eventually push the U.S. to institute a value-added tax.

Meanwhile, companies are facing much more aggressive enforcement from the Internal Revenue Service. The IRS is responding to Congress' demand that it narrow the gap between the amount it's owed and what it actually collects, Arnold says.

And it's not just the IRS that companies should be wary of. States and municipalities, also facing budget shortfalls, are stepping up enforcement as well. "You're going to see a lot more people spending a lot more money defending against challenges by the state tax authorities," says Richard Husseini, a partner in the tax department of Baker Botts in Houston. "People need to pay a lot more attention to their state tax planning."