Justice Secretary Hernando Perez said the Bureau of Customs has filed a graft suit before the Office of the Ombudsman and an administrative complaint before the Office of the Court Administrator against judge Arnulfo Cabredo, of Tabaco, Albay province.
Cabredo allegedly allowed a ship smuggling rice worth P50 million to elude customs authorities.
The government is also preparing to file criminal and administrative charges against Olongapo judge Eliodoro Ubiadas for helping a suspected smuggler get away, and against Pasig City judge Rodrigo Lorenzo for allegedly freeing six Chinese nationals accused of drug trafficking.
President Arroyo had earlier ordered Perez to press charges against the three judges in line with her campaign to root out so-called "hoodlums in robes" in the judiciary and curb the countrys crime problem.
"We cannot tolerate this. We will no longer be masochists about this. We will be pressing charges. So this is what were doing to fight corruption in the judiciary system," Mrs. Arroyo told reporters in a recent briefing.
In the case against Cabredo, authorities said he issued a temporary restraining order last year to prevent the Bureau of Customs from seizing a vessel, the M/V Criston, which was carrying 35,000 sacks of suspected smuggled rice.
That enabled the cargos consignees, Antonio Chua and Carlos Carillo, to rename the vessel to M/V Neptune Breeze and elude authorities.
In Ubiadas case, Perez said he was also accused of helping another suspected smuggler in Subic, Zambales, and thwarted what could have been one of the biggest seizures by the Bureau of Customs.
On the other hand, Lorenzo was held liable for granting bail to Chinese nationals Chua Chu Li, Huang Hongwei, Joey Lu, Xingfu Wang and Tomas Lu, who were all facing drug trafficking charges, a non-bailable offense.
Meanwhile, Perez said the Department of Justice has also approved the filing of administrative charges against a La Union state prosecutor, Oscar Corpus, for downgrading a non-bailable case that allowed two of seven Chinese nationals, accused of kidnapping a young woman late last year, to post bail.
Corpus was ordered by the department to justify why two of the suspected kidnappers, Zhang Du and Henry Ong, were allowed to post a P100,000 bail each and their five co-accused were not.
The department said according to the evidence Du should be charged as a "co-principal and be liable in the kidnapping of Rowena Jacky Tiu."
Police arrested the suspects at the Westin Philippine Plaza in Pasay City after the victims family paid ransom. The P10 million ransom was recovered.