He was the Secretary of the Department of Transportation and Communications (DOTC) of the Philippines under the administration of President Benigno Aquino III.

Jun then proceeded to Cornell University in Ithaca, New York, and completed a master's degree in electrical engineering (1989 – he was also a fellowship awardee).

In 2009, he among with fellow representatives of Cavite – Elpidio Barzaga, Jr. and Jesus Crispin Remulla — authored the biggest congressional reapportionment in the history of the Philippines by passing Republic Act No.

On October 12, 2012, Abaya was appointed by Benigno Aquino III as the Secretary of Transportation and Communications, succeeding Mar Roxas.

[2] In February 2016, the Philippine Senate released a report stating that Abaya and other DOTC officials "may have violated" the Anti-Graft and Corrupt Practices Act in relation to questionable contracts with the subsequent maintenance providers.