The Control Yuan ordered major corrective measures regarding the project three times in 1999 alone, finding that the construction permit was improperly issued, that the environmental impact assessment was made on an incorrect basis, and that proper provision had not been made for safeguarding a Ketagalan aboriginal archaeological site. These instances are taken as proof by antinuclear groups of the illegality surrounding the project.
期間，監察院並針對核四案於八十八年提出三大糾正案，包括建廠執照不當發放，糾正環評不確實，並於十一月提出凱達格蘭族文化遺址糾正案，皆是反核團體掌握核四廠違法的證據。