In the previous games, loading up a colony ship (or troop transport) with population and sending it to the other planet would do the trick, but it doesn't seem to work in GalCiv 3 yet.
I've sent a fully loaded colony ship to one of my colonies, but it didn't increase the local population. When it tried to "eject" the ship, afterwards, the game was acting as if the ship was empty. So, in effect, I just lost 2.5b people.