Have the port closed
From Create Your Own Story
"Only close the port for the next few hours," you advise. "Give no reason, or make one up. Anyway I doubt many ships will try to set sail in the middle of the night. But if we arrest von Carstein's supporters, they'll know that something is afoot. And if the Princess gets involved, the whole thing will become political. We all know that politics must never interfere with a military operation."
"Yes, that's wise," agrees Valerio. "I'll close the port immediately and launch a search of the sewers in an hour."