Gotabhaya Rajapaksa is charged with allowing a private firm to establish a floating armoury.
It is claimed the move deprived the state of more than $75m (Â£57m).
Mr Rajapaksa, who denies wrongdoing, served as defence secretary during the presidency of his brother, Mahinda Rajapaksa, which ended last year.
The charges were filed in a Colombo magistrates court by a special anti-corruption commission.
The discovery of the floating arsenal off southern Sri Lanka, and of another weapons haul in the capital, came in the days after Mahinda Rajapaksa was voted out of office.
Rajapaksa family's crashing fall from grace
Private firm Avant-Garde Security Service said the weapons were for escorting commercial ships, but police said they received complaints that the firearms were used for intimidation.
Gotabhaya Rajapaksa has also been dogged by accusations, which he denies, of human rights abuses linked to the final defeat of Tamil Tiger militants in 2009.
Several other members of the Rajapaksa family are also under investigation over alleged corruption.
Earlier this month, Namal Rajapaksa, the eldest son of Mahinda, was arrested on suspicion of money-laundering. He denies wrongdoing.
Namal's brother, Yoshitha, faces money-laundering charges while Mahinda's other brother, Basil, the former economic development minister, has been arrested three times over suspected misuse of funds and money-laundering. He is currently on bail.
Sri Lankan President Maithripala Sirisena has promised to investigate claims that members of the Rajapaksa family siphoned off billion of dollars of public money during Mahinda's nearly 10-year presidency.
The former president, now an opposition lawmaker, has also been heavily criticised over alleged human rights abuses by the Sri Lankan military during a long-running war with Tamil separatists.
One of Sri Lanka's most controversial politicians has been charged with corruption involving the illegal transfer of state-owned weapons.