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Clarke will end his career, which spanned three administrations, at the National Security Council.
His career was also characterised by a concerted effort to enhance the government's relationship with the private-sector operators of the critical infrastructures.
Howard Schmidt, Clarke's deputy on the Critical Infrastructure Protection (CIP) Board, is likely to move into the chairmanship position.
Schmidt has also been added to the shortlist of candidates for a senior assistant or deputy assistant secretary position in the Department of Homeland Security.
John Tritak, the director of the Critical Infrastructure Assurance Office (CIAO) at the Department of Commerce, is to become the assistant secretary for cybersecurity at the Department of Homeland Security.
The CIAO and the CIP Board are both expected to become part of the Department of Homeland Security.