The Panamanian- registered container ship COSCO ASIA came under fire on Saturday in a northern section of the canal, a major global trade artery secured by the Egyptian armed forces.
"There was an attempt to disrupt security in an area called el-Qantara as they fired at a ship in an attempt to halt (traffic on) the waterway," said the army source.
"Three were arrested and they have been dealt with ... This attack could not have harmed the ships."
The head of the Suez Canal, Mohab Memish, earlier said terrorists - possibly Islamist militants - had carried out the operation. Canal authority sources said a rocket-propelled grenade was used in the attack.