The Department of Homeland Security’s chief information officer, Richard Spires, resigned on Tuesday after nearly two months on leave for undisclosed reasons.

Deputy CIO Margie Graves is serving as acting CIO, a Homeland Security official said.

Spires, whose last day of federal pay will be May 17, said in an e-mail to Homeland Security officials: “I have served as the department’s CIO for more than 3 1/2 years, and I take pride in working with you to have IT more effectively support the Homeland Security missions and businesses as we also have worked to more efficiently deliver our services.”

Homeland Security has maintained that Spires went on elected leave beginning March 15, but rumors have surfaced that the decision was not his own.

Reports from FCW, a news outlet covering federal technology issues, suggest Spires butted heads with Secretary of Homeland Security Janet Napolitano over budgeting and policies toward IT purchases.

Rep. Bennie Thompson (D-Miss.), ranking member of the House Homeland Security committee, sent a letter to Napolitano in April requesting an explanation by May 6 for why Spires was on leave. Homeland Security did not meet that deadline, according to FCW.

For more federal news, visit The Federal Eye, The Fed Page and Post Politics. To connect with Josh Hicks, follow his Twitter feed, subscribe to his Facebook page or e-mail josh.hicks@washpost.comE-mail with news tips and other suggestions.