The Gay and Lesbian Equality Network (Glen) has said it is satisfied that all grants received have been used for the intended purpose and it has no reason to suspect there has been any misappropriation of funds.
In a statement from the charity's board, it said it had put in place new financial procedures to enhance its administrative systems including the appointment of specialist accountants.
The Charities Regulator has directed Glen to provide specific information including financial reports, details of staff credit cards and the report of an independent auditor.
The direction stretches back three years to 2014.
The HSE has also withheld some grants and has said it is in communication with Glen about 2017 funding.
Glen said today it was fully cooperating with the regulator.
"The board is satisfied that all grants received have been used for the intended purpose and has no reason to suspect there has been any misappropriation of funds," said the statement.
The charity also confirmed that its Executive Director was resigning from her post.
"Áine Duggan, Executive Director, has decided to resign her post. The board acknowledges the contribution to our internal review," said the statement.
"We will be making an interim appointment following the departure of the current Executive Director.
"We are grateful to our partners and to the agencies who continue to support our work and look forward to working together in the future," the statement added.
