After Edsa II, Defensor was appointed as Secretary of the Housing and Urban Development Coordinating Council by President Gloria Macapagal-Arroyo. He held that post until August 2004 when he was appointed Secretary of the Department of Environment and Natural Resources. In the 2004 presidential election, he served as the official campaign spokesperson of President Arroyo. After his tenure as DENR Secretary he was appointed Presidential Chief of Staff. He resigned that post on February 10, 2007 to campaign for a post in the senate. In June 2008 he was appointed head of the Ninoy Aquino International Airport International Passenger Terminal 3 by virtue of the June 9, Executive Order No. 732 The order provides for the NAIA-3 opening based on decisions of the Supreme Court and applicable laws. On October 9, 2008, Defensor was named acting chairman of the Philippine National Railways.
Senate candidacy
Defensor was among the first to file for candidacy for the senate on February 12, 2007. He employed popular gossip show host Boy Abunda as his campaign manager.
Controversy
Involvemet in ZTE-NBN scam
Mike Defensor, on July 4, 2008 filed 6-page perjury lawsuit Friday versus Rodolfo Noel Lozada for "testifying under oath that he had paid Lozada P 50,000 to change his statement that he was not kidnapped at the Ninoy Aquino International Airport when he arrived from Hong Kong at the height of the Philippine National Broadband Network controversy."
Defensor was the three Congressmen against the ABS-CBN along with Sagip partylist Rep. Rodante Marcoleta and Cavite Seventh District Rep. Jesus Crispin Remulla, Defensor inititiates online forum via Zoom and streamed live via Facebook along with Representatives Marcoleta, Remulla, Yedda Romualdez, Jonathan Sy-Alvarado, Dan Fernandez, Inno Dy and Alfred delos Santos discussing the fate of ABS-CBN, on July 18, 2020 they discussed the potential takeover of the ill-fated station due to alledged tampered torrens title, fine for alledged ilegal sale of ABS-CBN TV Plus for almost P 2 trillion, and the total closure of Sky Cable, pro-ABS-CBN advocate Christine Bersola-Babao slams the forum and called the Congresspersons as "evil".
On December 4, 2007, Mike Defensor quietly joined / was nominated to the board of directors of Petron Corporation. Defensor had been frequenting Macau. Boncodin stated that Mike was invited to the board by Nicasio Alcantara, government’s team head / Chair, Petron. Membership in the Petron board is a lucrative job, as Defensor was offered a board seat in sequestered United Coconut Planters Bank. Defeated administration candidate, former senator Ralph Recto joined the board of Union Bank, controlled by the Aboitiz family.