The Agreement also prevents US military personnel from being tried in Filipino religious or military courts[1][V 11]; requires both governments to waive any claims concerning loss of materials (though it does require that the US honor contractual arrangements and comply with US law regarding payment of just and reasonable compensation in settlement of meritorious claims for damage, loss, personal injury or death, caused by acts or omissions of United States personnel)[1][VI]; exempts material exported and imported by the military from duties or taxes[1][VII]; and allows unrestricted movement of U.S. vessels and aircraft in the Philippines.

[6][7] On January 18, 2006, the US military maintained custody of four troops accused of rape while visiting Subic Bay during their trial by a Philippine court.

A second Philippine court case under the VFA is the one following the death of Jennifer Laude, also involving a US Navy ship docked at Subic Bay.

Vs. President Gloria Macapagal-Arroyo, et al. submitted on January 2, 2007, was decided on February 11, 2009, again by the Supreme Court sitting en banc.

In deciding this second challenge, the court ruled 9–4 (with two justices inhibiting) that, "The Visiting Forces Agreement (VFA) between the Republic of the Philippines and the United States, entered into on February 10, 1998, is UPHELD as constitutional, ...".

The decision continued, specifically relating to matters relevant to the Subic Rape Case, "... the Romulo-Kenney Agreements of December 19 and 22, 2006 are DECLARED not in accordance with the VFA, and respondent Secretary of Foreign Affairs is hereby ordered to forthwith negotiate with the United States representatives for the appropriate agreement on detention facilities under Philippine authorities as provided in Art.

"[13] UP professor Harry Roque, counsel for former senator Jovito Salonga, one of the petitioners in the case, said in a phone interview regarding the decision on the constitutionality of the VFA.

"[14] On February 11, 2020, Philippine President Rodrigo Duterte formally announced to the United States embassy in Manila that he was ending the pact, with termination to take effect in 180 days unless agreed otherwise during that time.

[17] In a speech on February 12, 2021, President Duterte addressed himself to the US on this saying, "I would like to put on notice if there's an American agent here that from now on, you want the Visiting Forces Agreement done?