"The reasons are once again incorrect reports concerning the payment of wages and social security deductions," said a statement on the SFV website.
It added that the problem, reported by the Swiss league's licensing committee, concerned the payments for November.
Neuchatel have suffered two four-point deductions and Swiss media have reported that a further penalty could result in the club being expelled from the country's Super League, which is on its winter break and restarts on February 4.
The Swiss Players' Union complained this month that the Neuchatel squad were owed two months' wages and described the situation as "unacceptable".
Chagaev has since sacked four coaches and faced a boycott by fans. He also fired the club's administrative staff last year and ended all the sponsorship contracts.
In November, Neuchatel survived a request for bankruptcy made by a players' agent who took the club to court alleging that he was owed 400,000 Swiss francs.
