I do not have much bonsai experience. My Fujian Tea Leaf tree started sprouting mushrooms about two weeks ago, possibly because of overwatering as it was left in a container of water while I was out of town. The mushrooms haven't gone away. I'm planning on repotting it into inorganic soil, but while waiting I have just been cutting the tops off the mushrooms so they hopefully cannot spread more.

Is this a good plan? What else should I do?

I think fujian tea is a type of tea, this is a plant called fukien tea.

Do not repot until early spring, but that might not even be necessary. I can't see any mushrooms nor do I know how to identify them, so I can't be sure.

Can't identify from the one leaf, but Fukien Tea is likely. There are leaves thaqt look dying too, nothing on the soil, but if it was left in water then there is a possibility that the roots have been damaged. Leave it to get almost dry before watering again. If it persists then you will need to re pot.

BonsaiLearner wrote: I think fujian tea is a type of tea, this is a plant called fukien tea.

Yes and No, Fujian tea = Fukien tea.

LilacGalaxy wrote: I do not have much bonsai experience. My Fujian Tea Leaf tree started sprouting mushrooms about two weeks ago, possibly because of overwatering as it was left in a container of water while I was out of town. The mushrooms haven't gone away. I'm planning on repotting it into inorganic soil, but while waiting I have just been cutting the tops off the mushrooms so they hopefully cannot spread more.

Is this a good plan? What else should I do?

Did you do any searching on the web? I found this after 20 seconds. Does this help?
www.bonsai4me.com/AdvTech/ATBonsaiMushrooms.html
Try to identify the mushrooms and take note of the environment that the tree is in. Let us know what you come up with.

I did find a lot of similar information; however, what I could not find was a picture that looked like the specific species of mushroom (if the picture above is unclear, it is very similar in size and colonization pattern as the last group of mushrooms in your link, but gray, taller, and with thinner stems). It's good news and new information that apparently the mushrooms are not harmful, but do you know about the affects of rotting in the tree that the mushrooms indicate? Or how significant of a problem root rot would be on a Fukien?

I don't have the answers about the type of mushrooms that are on your tree. Like I said.. you'd have to look them up yourself. I've also not had the problem myself, so I can't suggest how to treat the mushrooms or the tree or the effects of those particular mushrooms on your tree. sorry.
The point that I failed to make, is that YOU have to research this yourself because of your individual circumstance. Unless someone on here has experienced the exact or (closely similar), situation. I was just trying to point you in a good direction.
I would like to see a picture of the tree!

LilacGalaxy wrote: It's good news and new information that apparently the mushrooms are not harmful, but do you know about the affects of rotting in the tree that the mushrooms indicate? Or how significant of a problem root rot would be on a Fukien?

Indeed the mushrooms (or actually the fungus in the soil) are not harmful for the tree, but as you already noticed, they are living of something in the soil, that may be rotting wood. If that are the roots of your tree, than that is a significant problem that may kill the tree.

Check your watering methods (look up fukien tea tree care, under the species guidelines on this page)