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A Conference spokesperson said: "The Conference Board were always clear and unanimous in their view that the England Manager should be independent of any club and formally took that opinion to the FA.
The number two boss was unhappy with the allegations he also was using the job to tap into other clubs' players.
Inglethorpe told the Exeter Express & Echo: "There was a poll run which questioned my integrity.
"Some people claimed the role gave me an unfair advantage, but that is just not true."
He added: "Are you saying that because Steve McClaren is involved in the England set-up that everyone is going to go to Middlesbrough, and because Peter Taylor is involved with that England Under-21s that Hull are going to get the best players.
"I am really disappointed but I don't feel as though I have been given much choice.
"I leave with a heavy heart. I really enjoyed my time with the England set-up and learned a great deal in the process.
"It is an honour for any manager to represent their country, whatever the level, and it gave me real pride.
"But I am not willing to put up with people looking down their noses at me - so I will have no further involvement with the set-up."