Employment Court chief judge Christina Inglis last week found that six women at the religious commune on the West Coast were actually employees.
Gloriavale says the judge got it wrong and it will be appealing.
Charities Services has an open investigation into Gloriavale, with general manager Charlotte Stanley saying it was carefully considering the findings of the Employment Court.
"Our initial assessment of the judgment raises concerns across a range of matters of interest to various government agencies.
"In terms of Gloriavale meeting its obligations under the Charities Act 2005, we have an open investigation into this registered charity."
The investigation would be conducted under the Charities Act mandate and required consultation with other relevant agencies.
Registration as a charity brings a range of benefits, including tax exemptions and donor status.
To remain registered, charities must advance charitable purpose, report annually, and not engage in conduct that constitutes serious wrongdoing, as defined in the Act.
Should a registered charity be found to have engaged in serious wrongdoing, they may be de-registered by the independent Charities Registration Board.
"As this matter is now subject to our regulatory processes, it is not appropriate to make any further comment. We will provide further updates as they become available."
Gloriavale kept its charitable status despite a 2016 Charities Services investigation.
It announced last year it was reopening the inquiry.
Meanwhile, Gloriavale School is under review by the Education Review Office, the Ministry of Education has confirmed.
