The tax collector should be able to use the resources in the city and convert them to paying taxes that are collected by the person who owns the fortress. For example 10000 of each resource collected by the tax collector could be used for paying 1% tax. 20000 of each resource could be used to pay 2% tax... and so on up to 50000 to the max 5%.

This of course would only work if your tax collector in the city is a master knowledge hero.