In 1961, Climaco gave up his post as mayor for an unsuccessful run for the Senate under the Liberal Party. After his defeat, he was appointed by President Diosdado Macapagal as Commissioner of Customs. As Customs Commissioner, he brought in cadets from the Philippine Military Academy, vaunted for their idealism and honesty, to work in a Bureau of Customs which had long been reputedly corrupt. He again ran and lost for a Senate seat in 1963. Climaco then was appointed as a Presidential Assistant under Macapagal.