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.

The 37-year-old made 64 appearances for his country, including three at the 2006 World Cup, and is Poland's most-capped goalkeeper.
Boruc has been mainly used as a back-up keeper to Lukasz Fabianski and Wojciech Szczesny in recent years.
"It has not been an easy decision for me and has been one that I've taken incredibly seriously," he said.
"However, after much thought and consideration I feel that now is the right time in order to focus fully both on my family and club career at AFC Bournemouth."

Health Inspectorate Wales said Wrexham Maelor Hospital staff were under "considerable pressure" for long periods as ambulances waited outside.
It said inspectors were told the situation was not unusual.
Betsi Cadwaladr University Health Board said it was working to manage the pressures.
Inspectors visited the A&E unit and another ward on 30 September and 1 October last year and have released reports about what they found.
Despite the pressures in A&E they said staff were observed to be effectively prioritising clinical need and patient care.
On the Mason Ward, inspectors found patients to be well looked after and said staff were committed to providing good standards of care.
Angela Hopkins, executive director of nursing and midwifery at the health board, said its hospitals were experiencing growing demand like the rest of the UK.
"We are focussing on the improvement of emergency department and ward processes for both admission and discharge to reduce delays," she said.
"We are increasing the numbers of nursing staff and extra beds have been opened.
"We are also working in partnership with local authorities and the Welsh Ambulance Service to ensure that the system works more smoothly to improve patient flow through the hospital."
One of Sri Lanka's most controversial politicians has been charged with corruption involving the illegal transfer of state-owned weapons.
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Bournemouth's Polish goalkeeper Artur Boruc has announced his retirement from international football.
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An unannounced inspection of an under-pressure A&E unit at a north Wales hospital led to concerns for patient safety, a watchdog says.