Health New Zealand says it has received $419m in pay equity reimbursement from the government.
Earlier, it had said it did not receive this in the last financial year as expected, driving up its deficit.
Chief executive Margie Apa said on Thursday the settlement had been received as equity funding.
"While the receipt of this settlement does have a positive effect on our cashflow, it does not impact our budgeted deficit of $499m" for 2024-25, she said in a statement to RNZ.
The agency must continue to bring down the "run rate deficit" of $150m a month, she added.
The government said on Wednesday night it had given Te Whatu Ora the funding, and that while it would have helped the agency's financial result for the year to 30 June, it would not have meant a return to surplus.