Singapore's foreign ministry said Singaporean Tan Hui Tin and the locally registered Chinpo Shipping Company Ltd had been charged by the public prosecutor and would face court.
A North Korean ship headed from Cuba to North Korea was seized in June last year by Panamanian authorities, who suspected it was carrying drugs.
Two Cuban fighter jets in perfect condition, missiles and live munitions were discovered beneath the Chong Chon Gang's cargo of sugar.
Panama said the weapons violated UN sanctions restricting arms trading with North Korea.
Singapore's foreign ministry did not specify what charges were filed.