The allegation centers on Harris’ response to an email from FC United supporter Aled Duckfield complaining about the NPL’s decision to change the location of FC United’s match against Stockton Town to nearby Curzon Ashton on April 21.
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The match has been postponed six times due to problems with FC United’s pitch at Broadhurst Park.
In his email to Harris, Duckfield called the decision “diabolical” and accused the NPL of “incompetence” and “lack of governance.”
Harris’ alleged response contained abusive language directed at Duckfield, who said he was “surprised” by the response.
The NPL Board met on Friday morning to discuss the matter, which is also the subject of an investigation by the Football Association.
“Following a board meeting, the Northern Premier League can confirm that chairman Mark Harris has been relieved of his duties with immediate effect, pending a full disciplinary investigation,” an NPL spokesperson said.
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Harris declined to comment on the alleged email, but BBC Sport was told it was reported to the FA.
The FA said: “We can confirm that we are investigating this matter. As this is an ongoing process, we are not in a position to provide further comment.”
Harris is a highly respected figure within non-league circles.
He was appointed Chairman of the NPL in 2009. He also sits on the FA National Leagues Pyramid Board.
FC United argue that the decision to postpone the match against Stockton could affect their title chances (they would go top if they win their remaining match) and also significantly affects them from a financial perspective.
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The club lost at Broadhurst Park on Monday to title rivals Hednesford Town and have one other league match, a local derby against Hyde United on April 18, which has not been moved.
The NPL feels it cannot afford to risk a postponement given the season ends on April 25 and the excellent match has significant implications for both the title and the playoffs.
FC United suggested carrying out a pitch inspection at Broadhurst Park the day before the match and changing it if the surface was deemed unplayable or the match was at risk. This was rejected by NPL.
Gainsborough Trinity and Warrington Rylands, who are involved in a battle for play-off positions with Stockton, have also told the NPL they have “serious concerns” about the game being moved.
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There has been no indication that the NPL will change the match again, and the issue is considered separate from the allegations against Harris.
“The language used in the email attributed to the NPL chairman is clearly completely unacceptable; however, it reflects the attitude that many involved in the governance of the game have towards fans,” an FC United spokesperson said.
“It also raises fundamental questions among supporters about whether decisions involving FC United can be approached with the true impartiality that the role demands. In light of this email, many will be understandably concerned.
“We will seek urgent clarification from the Northern Premier League.”