Justice Britto of the Panaji bench of the Bombay high court recused himself from hearing Pacheco's plea without assigning any reason.
Pacheco is in the custody of the crime branch for allegedly abetting the suicide of his close friend Nadia Torrado, 28, who died after consuming poison on May 30.
Justice Britto had earlier recused himself from hearing Pacheco's anticipatory bail plea last month when the former minister was on the run, also without specifying a reason.
Pacheco's counsel Amit Palekar said he will now write to the chief justice of the Bombay high court for referring the bail application to a new bench.
The 46-year-old NCP legislator was arrested on July 8 and his police remand expires on Friday. He will be produced before a local court for extension of remand, sources said.