I assume we're talking about Port Royale 1 here. I searched a bit and found some mission guides I had archived, as they where hard to find in the Internet. Here's what could be the mission you're referring to (you get this one in the Inn):
Attack a convoy in repair
A fellow in the inn spins a sob story about a nation being at war but unable to afford to attack a fleet that's in a harbor for repairs, then butters you up by telling you you're considered to be quite dangerous, and offers to pay you for attacking the fleet. He'll offer 20,000 gold for each ship of the fleet you sink. To attack the fleet, you must wait until the fleet is actually in the harbor-it will be named as a military convoy. Then select to attack the nation that controls the harbor, and attack from the sea. You'll receive a message that there is a military convoy you must defeat first-that's your target. Why the fleet is in for repairs is beyond me, since it seems to be quite fully manned and repaired, but that's neither here nor there. To get paid for the mission, you must sink-not capture or loot-the ships in the convoy. Once the convoy is defeated, you'll receive the cash for each ship you sank. Notice you can capture the ships if you wish, but you only get paid for the ones you sink. Also note that sinking a country's military convoy tends to upset them greatly. After you've beaten the military convoy, you'll find yourself preparing to attack the town from the sea. At that point you can simply flee the battle or continue your attack.
Mission Accomplished:
You sink at least one of the ships and receive 20,000 for each ship sank.
Mission Failed:
You don't sink any of the ships, and don't receive any money.
Assessment:
If you're good at sea battles and don't mind the hit to your reputation for sinking a country's ships, it's an easy 20k per ship. If you're not so good at sea battles, then you'll find yourself in over your head, as the military convoys are pretty stout.
Information:
Your logbook will contain when and where the fleet will be, and after completing the mission, the total you were paid is entered.