Pacheco, who was charged with culpable homicide following the suspicious death in Chennai of 28-year-old Nadia Torrado, was underground for nearly a month.
Margao district and sessions judge U.V. Bakre, who heard Pacheco's interim bail plea, reserved the order until Monday afternoon and sent the former minister to two days judicial custody.
Pacheco's application for anticipatory bail was rejected by the Supreme Court Thursday.
Pacheco and his aide Lyndon Monteiro face culpable homicide charges in connection with Nadia's death May 30. Nadia died after consuming rat poison following an apparent row with Pacheco.
The former minister went underground after being grilled by the Crime Branch for over nine hours June 4.
Monteiro, who was also missing for nearly a month, appeared before the Crime Branch officials Saturday, who interrogated him.