WASHINGTON, Jan 17 (Reuters) - Royal Dutch Shell has paid $25 million to the U.S. government to resolve claims that the company underpaid royalties on federal offshore oil and gas leases, the U.S. Interior Department said on Tuesday.

The settlement applies to royalties paid in cash and those paid in oil and gas through the now defunct "royalty-in-kind" program for Shell deepwater leases in the Gulf of Mexico between 2000 and 2008.

Interior's Office of Natural Resources Revenue said audits of Shell's leases had uncovered "various valuation issues."

"This settlement further demonstrates that ONRR's audit program is working diligently to collect every dollar due from energy companies operating on federal leases," said Greg Gould, acting deputy assistant secretary for natural resources revenue.

Shell said following negotiations over the complex royalty calculations, it believes the settlement is "fair and appropriate."

"Shell's policy is to pay all royalties correctly," Shell spokeswoman Kelly op de Weegh said in a statement. "Should issues arise, we seek to clarify matters through consultation and compromise."

Last year, Shell agreed to pay the government nearly $2.3 million to settle separate claims that several of its affiliates underpaid royalties due for natural gas produced on federal leases.

(Editing by Lisa Shumaker and Dale Hudson)

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