Rodriguez also was appointed as the head of the Bureau of Immigration by President Joseph Estrada in 1998 and served in that capacity until 2001.

From 2007 to 2016, Rodriguez was elected as the representative of the second district of Cagayan de Oro in the 14th-16th Congress, ranking second among 268 congressmen on the most number of bills and resolutions filed at 554, of which 53 became Republic Acts.

On June 19, 2009, Rodriguez received a Certificate, Leaders in Development from the John F. Kennedy School of Government of Harvard University.

In 2015 Justice Undersecretary Justiniano amended a complaint against Representative Rodriguez for his part in the 2013 Pork Barrel Scam.

When the 70 congressmen denied ABS-CBN's hopes of renewing its legislative broadcast franchise on July 10, 2020, he slammed the vote because the solons defied the evidence that the network has not committed numerous violations.

In 2011 he was conferred a degree of Doctorate of Humanities (Civil Law), Honoris Causa, by the Central Mindanao University.

Rodriguez was also conferred a Doctor of Laws (Honoris Causa) degree by the University of Negros Occidental - Recoletos (UNO-R) in 2012.