Sanjeewa Pushpakumara said the film, Flying Fish, sought to depict reality and was based on his own experiences growing up in Sri Lanka’s war zone.
The film was banned on Friday after being shown at a festival promoted by the French embassy in Colombo.
A government spokesman said the film was “illegal” and used images of the army uniform without permission.
In a statement issued from South Korea, where he is based, Sanjeewa Pushpakumara denied discrediting the military and said he sought to depict reality “in a humane and artistic way”.
He denied any links with the Tamil Tigers or non-governmental organisations, and dismissed state television broadcasts which had alleged such ties.
Police are now holding what they call a “fact-finding investigation” into the film and some of its production staff have been questioned.
The distribution and screening of the film had been stopped in Sri Lanka, government security spokesman Lakshman Hulugalle, confirmed on Monday.
The Sinhala-language film was made in 2011 and is set against the backdrop of the country’s brutal civil war. The film is said to portray bad behaviour by both soldiers and Tamil Tiger rebels, the BBC’s Charles Haviland in Colombo reports.
The Sri Lankan state venerates its armed forces and any message that contradicts this is liable to fall foul of the authorities, our correspondent adds.