NRW’s responsibilities include managing forests, responding to floods and granting environmental permits.
Its annual accounts say an HMRC investigation revealed a “potential liability” related to specialist contractors.
NRW said it paid the £19m “without any admission of liability” for unpaid income tax, National Insurance contributions or the apprenticeships levy.
The money is also meant to cover interest payments, but discussions about the final debt are continuing and a “wide range of values are possible”.
The Welsh government said it would discuss how NRW can repay it when there was a final bill to HMRC.
NRW said it could provide no further details while the case continues.
In a statement it said: “We continue to discuss this matter, and the extent of the potential liability, that may be owed in order to achieve a resolution.”
