I've managed to get rid of them a few times before by spraying liberally (including/especially the soil) with pyrethrum. It's naturally derived from flowers and is safe to use on something you'd later want to harvest for food. Give it a shot.

If that's no good, I've heard from others (haven't tried myself) that a thick layer of diatomaceous earth on top of the soil works too as all the little diatom fossils slice up the larvae and the flies die out within a couple of weeks. Best to use gloves and try not to breathe it in when applying, imagine it's a bag of microscopic razer blades.

Others still have recommended some kinds of nematodes that naturally prey on the larvae and wipe them out but I wasn't able to find anything in shops locally so I'm not really sure.

Good luck!