Nonprofit workers who received the correspondence described the correspondence as a "goodbye letter" and a "farewell."
The agency said in the letter, "In the long term, extractive industry transparency should not be confined to EITI reporting," but "rather be recognized" as "an integral part of how Government manages."
Asked for clarification by CNBC, the Department of the Interior declined to outline whether it meant the agency would drop efforts to comply with EITI in favor of incorporating some EITI standards into its own reporting requirements.
Swift said the nonprofits were either issuing deliberately misleading characterizations of the conference call or had misunderstood the Interior officials.
She further said the EITI Board in Oslo, Norway has pointed to the U.S. EITI website as "an example of the best way to make data publicly available" and approved it "as a compliant reporting system."
That is only half true, according to the EITI Board.
The EITI Board has indeed "highlighted" the U.S. website, but it has not validated it as compliant, said Sam Bartlett, regional director for EITI who oversees implementation.
The challenge for the U.S. compliance with EITI remains securing industry participation, including getting more companies to report corporate income taxes, he said.
— CNBC's Katie Little contributed reporting to this story.