District Judge B P Deshpande rejected the bail petition filed by Alemao, who is currently lodged in Colvale prison.
The former minister is accused of accepting bribe from US-based Louis Berger company to award them consultancy for Water Augmentation and Sewerage Project funded by Japan International Cooperation Agency (JICA).
While refusing the bail, the court did not pronounce the detailed verdict, which is likely to be uploaded on the court's website later in the day.
The district court had earlier granted anticipatory bail to former Chief Minister Digambar Kamat in connection with the same case.
Alemao, who moved the bail plea last week, had argued that there should be parity in justice as he was facing the same charges as Kamat, who was granted anticipatory bail.
Alemao is booked under IPC section 120-B (criminal conspiracy) and sections 7, 8, 9 and 13 of the Prevention of Corruption Act in connection with the case, which allegedly took place when he was PWD minister.
The Crime Branch had last week appealed before the Goa bench of Bombay High Court against the anticipatory bail granted to Kamat by the district court.
The police had recently slapped an additional charge of 'causing disappearance of evidence' against Kamat under section 201 of IPC. Earlier, he was charged under IPC section 120-B (conspiracy) and the Prevention of Corruption Act.
Kamat was Goa Chief Minister when the alleged bribe was given in 2010.
Police have so far arrested Churchill Alemao, former vice president of Louis Berger Satyakam Mohanty, head of JICA-aided project in Goa Anand Wachasunder and alleged hawala dealer Raychand Soni in the case.
Mohanty was later granted bail on a surety of Rs one lakh and barred from leaving India.
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