One NEC member told the Independent it could be NEC members who bear the financial burden, saying: "If it’s really bad then it opens up all sorts of possibilities and it has been raised that the whole thing could basically bankrupt the party.
“People are really worried."
The EHRC announced its inquiry in May and is expected to produce a report with recommendations next year.
Rising staff costs helped push Labour into the red last year, making a loss of £655,000 compared with a surplus of £1.45 million the year before.
Speaking to the JC last month, deputy leader Tom Watson said he had been kept in the dark about the party's response to the EHRC but revealed some of his "NEC colleagues" were due to give evidence themselves.