"There was no complainant and no aggrieved party, still people are arrested and put behind bars," Rajapaksa said.
Namal who is an opposition legislator was arrested and remanded on Monday over an investment project by Indian firm Krrish Group in 2013.
He was accused of misappropriating Rs 70 million (USD 500,000) obtained from Krrish. The project came to a halt after the Urban Development Authority imposed a fine on Krrish for failure to meet contractual obligations.
Namal's younger brother, Yoshitha had been previously arrested by the FCID and was let out on bail after being in custody over another business deal involving a sports television channel.
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Other members of the Rakapaksa family are also facing police investigations for alleged financial crimes. They include Rajapaksa, who was president for a decade until 2015, his brothers Basil and Gotabaya, and his wife Shiranthi.
The Rajapaksas claim that the investigations are a political witch-hunt against them and their sympathisers believe these allegations were brought to tarnish his name after he led Sri Lankan forces to victory over the LTTE rebels in 2009, ending a three-decade civil war.