Bottom of bowl is stained very much. Appears to be a defect in the the finish?

CRL soak

Use a product called "CLR"

might be just stained
get a good stain remover or drain cleaner and leave it sit for a while then flush
talk with a plumber as to possible solutions

You would have to determine what the stain is before an accurate answer on how to deal with it. Can you add a picture?

Probably a mineral buildup. Pour a bucket of water into the bowl so that the bowl flushes but does not refill with water. In other words you want as little water in the bowl as possible so it wont dilute the cleaner. Use an acid cleaner like lime away in the bowl. Let it set for several hours or over night,. then scrub with toilet brush. Lime away is fairly safe but try not to splash it on your clothes or yourself. Wash it away if you do.
You may have to repeat to finish the job.

Toto toilets usually have a very good porcelain finish. I would first try a toilet bowl cleaner or a rust remover such as CLR or Lime Away. DO NOT ! MIX ANY OF THESE CHEMICALS UNDER ANY CIRCUMSTANCES! Try one making sure to give it time to work then thouroughly flush the toilet before trying another. The brown stain may be rust or water scale. If the porcelain is actually gone replacing the toilet is probably the only fix. Hope this helps.
Bob

CLR .works well

My toilet had same problem:
I thought it was a clog in the drain pipe.
But the problem was clogged holes where water flushes into toilet bowl.

Here's how I fixed problem.
Purchase:
Gallon of CLR calcium-lime-rust remover from Home depot.
Pumice stone from hardware store.

Home supplies:
Cut off bottom of empty clorox bottle to make container for CLR
Old 3" paint brush you don't use for anything else to apply CLR
Small cup to pour CLR into toilet flapper opening

Steps:
Look inside toilet bowl under rim and see holes where water comes out
Use brush and apply CLR to holes where water comes out.
Use pumice stone to scrape ... pumice stone will not hurt toilet surface.
Flush toilet to clear holes so far.
Turn off water to toilet.
Open flapper to drain tank.
Keep flapper open.
Use cup and pour dose of CLR directly into flapper opening.
(You can also pour CLR down overflow tube... but flapper opening puts whole dose directly onto problem)
Pour another cup of CLR into opening.
Notice how CLR starts coming out the holes into bowl.
Pour CLR down flapper hole until it runs easy and fast out of holes.
Close flapper, turn on water, toilet fixed.

try clr in it worked for mine