To collect taxes from native races you must have 100 colonists ( one clan ) for every megacredit taken.
megacredits available from natives =
( native population ) * ( tax rate % ) * ( government factor % ) * 0.001
example:
planet: Kzin
8,000,000 natives
10% native taxes
Humanoid / Tribal
1200 Colonists
( 8000000 ) * ( 0.10 ) * ( 0.80 ) * 0.001 = 640 megacredits
If you have 64000 or more colonists ( 640 clans ) you will be able to collect the 640 megacredits from the native. Since you only have 1200 colonist on this planet you can only collect 12 megacredits. The natives will keep 628 megacredits and may still become upset with you for taxing them at a rate of 10%.
There is a switch in HCONFIG that that allows native races to be discovered from time to time on worlds without native life. They will be found only on worlds that do not already have native life.