The Marxist Janatha Vimukthi Peramuna (JVP) today complained to Defence Secretary B M U D Basnayake against Rajapaksa's son Yoshitha who is a Lieutenant in the Sri Lankan Navy.
They accused Yoshitha Rajapaksa of enlisting illegally and depriving qualified personnel of overseas training.
The JVP, said Yoshitha, 27, did not have the basic qualifications when he was recruited to the navy in 2006.
He was sent to the prestigious Royal Naval College at Dartmouth in UK for officer training shortly after enlistment, a privilege usually reserved for the best local cadet, the JVP said in its complaint to the Defence Secretary.
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"At Dartmouth too he failed many subjects," he said.
The Navy spokesman Kosala Warnakulasuriya said the former president's son asked to be discharged on January 9, soon after his father was defeated but his request has been turned down.
Rajapaksa has three sons -- Namal, Yoshitha and Rohitha.
The JVP has also lodged a complaint against Rajapaksa and his family members over graft claims.
In a related development, another Rajapaksa aide, former Sports Minister Mahindanada Aluthgamage's passport was impounded by anti-graft officials.
Since the former President's downfall, there have been allegations of widespread corruption and amassing of wealth by him during his 10-year-rule.
Fleets of expensive cars, a two-seater aircraft and several other valuables were found abandoned after Rajapaksa was defeated by his loyalist-turned-foe Maithripala Sirisena who defected and mounted a challenge in the January 8 polls.
Information on alleged properties of the Rajapaksa family is being regularly given to police since the advent of Sirisena-led new government.
Mahinda Rajapaksa ruled since 2005 and is credited with ending the LTTE separatist war.