They should have taken out the ship the moment they noticed it, and they noticed it quite early. The enemy commander was absolutely correct saying the Japanese were naive to leave them unchecked using environmental damage or whatever as an excuse. We saw in this episode at the latest that the enemy brought a whole fricking army with APCs and those battle mecha and lots of troops to the city. It was a war in the middle of a Japanese city, yet the Japanese couldn't afford to send in a single missile to take out the enemy command and cargo ship. It was utterly pitiful, even if they were victorious eventually and struck back highly efficiently. Not that the enemy ground troops would have been any better... But I guess an average Japanese author would be hard-pressed to write better than this considering pacifism is in their constitution.