The special royalties task force, established in December, includes auditors from the federal government, Montana and Wyoming.
A spokesman for Wyoming Gov. Matt Mead said no problems have yet been found.
Securities filings by Cloud Peak Energy show Asian exports accounted for 23 percent of the company's revenues but only 5 percent of its coal production through the third quarter of 2012.
In a letter to Salazar, Cloud Peak CEO Colin Marshall said the company considers transportation logistics work as "fundamentally different than our business of selling coal at the mine."
He said the company plans to list mining and logistics as separate businesses in its upcoming annual report.
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