(Dow Jones) Estate tax audits by the Internal Revenue Service are as aggressive as ever, and maybe even more so, despite the uncertain fate of the federal tax on estates of the wealthy.

The tax agency is challenging the way assets are valued and has not hesitated to reject certain favorite tax-reducing strategies reported on tax returns, according to some tax attorneys.

Family limited partnerships, popular tax-saving structures that have become controversial in recent years, top the list of items that are causing problems for taxpayers these days.

Tough audits come amid particularly odd circumstances for wealthy taxpayers. The federal estate tax has been repealed this year under an old law that Congress failed to fix. It is set to revert next year back to rates of 55% for estates of $1 million or higher, replacing 2009 rates of 45% for estates of $3.5 million and higher.

Stephen M. Breitstone, partner and head of the tax practice group at Meltzer, Lippe, Goldstein & Breitstone LLP in Mineola, N.Y., said he will work with clients to fight the outcome of two recent estate tax audits that, in his opinion, threw out family partnerships "without a proper legal basis for doing so."

The IRS is continuing to be aggressive in estate tax exams overall, said Laurie A. Urbanowicz, a certified public accountant at accounting firm Selznick & Co. LLP of Armonk, N.Y. As for its treatment of family limited partnerships, the agency "continues to come up with better arguments against them, and the courts are beginning to listen," said Urbanowicz.

The key to avoiding trouble with estate tax returns is to get good appraisals and document everything carefully. Estate tax attorneys sometimes must devote several months to cases because of their complexity.

The average amount of additional tax the IRS recommends taxpayers owe after an estate tax audit is $363,149, according to new data from the agency. The bigger the estate, the more the taxpayer ends up owing post-audit. However, several hundred thousand dollars in additional tax often represents a tiny fraction of the estate. Last year, a husband and wife wouldn't have owed estate tax unless they were worth more than $7 million.

How much extra tax gets collected after an audit depends on the kind of errors found and correlates to the size of the estate. Adjustments can be due to everything from math errors to missed or misvalued assets and inflated deductions, to the improper use of partnerships and other structures.

During her tenure as an estate tax attorney at the IRS, the agency did not reward auditors for finding large tax deficiencies, said Lorraine New, a Birmingham, Mich., attorney who was at the IRS from 1988 to 2007. Employees who never found adjustments, however, could find themselves in trouble because that indicated "they just were not looking or thinking," said New.