MANILA, Philippines—Malacañang Sunday challenged Ombudsman Merceditas “Merci” Gutierrez to prove her independence in handling cases that may be filed against former President Gloria Macapagal-Arroyo, even as lawmakers warned it would be difficult to impeach Gutierrez because Arroyo would block such a move.

President Benigno Aquino III’s spokesperson, Edwin Lacierda, said the proposed truth commission to be headed by former Supreme Court Chief Justice Hilario Davide Jr. would ensure th...