According to the China Post,

Many experts have suggested that, if the 337,000 invalid ballots cost the election of the "pan-blue" presidential candidate Lien Chan, the Ministry of Justice (MOJ) is to blame.

The MOJ, under minister Chen Ting-nan, has made the identification of invalid ballots more stringent.

The ministry has stipulated that a vote is valid if the stamp is made in the box above the photo of the candidate. The rule is sharply different from the one carried out by the Central Election Commission (CEC) for decades, allowing a ballot to be valid if the stamp is made over the candidate's name or its ballot number.