Justice K Ramakrishnan rejected the bail plea of Radhakarishnan, a contractor with the Malabar Cements, arrested on March 19 in Palakkad.
The CBI had opposed the bail plea and told the court that investigation was in progress and granting bail at this stage would adversely affect the probe.
It also informed the court that the deaths were a case of homicide.
Saseendran and his two young sons were founding hanging in their house in Palakkad on January 24, 2011. The incident had led to a public outrage with certain political quarters alleging that the company official had been under severe pressure to hide some of the corrupt deals involving contractors with "high connections.