Ultimately he needs a contract with whoever is paying his salary and his Non-B and Work Permit must be tied to that contract. That's the one that will be used officially when it comes to taxes, labour disputes or anything official. The fact that he signed a contract with the school makes him and the school liable should anything happen. The agent is just sitting back taking 4000 Baht straight off his currently contracted salary per month with no liability for them. The government will see the school paying him a certain amount which includes that 4000 Baht.

23 hours ago, jaffas21 said:

The agency has stated many times they are my employer to me personally,

If you signed an employment contract with the school then they are your employer.

20 minutes ago, LongTimeLurker said:

If you signed an employment contract with the school then they are your employer.

And they should be paying you the amount on the contract.

The 4,000 per month should be coming out of their pocket, not your salary.

5 hours ago, Raymonddiaz said:

I was hired in 2012 by an agency and i worked for a school in Nan. All my visa and work permit was handled by the school but i got paid by the agent. I signed a contract with the school only to get the paperwork done. Some agencies can't hire officially a foreign teacher so they use school names for that.

This makes the most sense.

 

But presumably you had a contract with the agency pre-dating the school "contract"? Whereas the OP hasn't stated anything about a contract with the agency.