The Government's forecast tax take fell in the first three months of the financial year, pushing the operating deficit before gains and losses higher than expected.
Tax revenue was $295 million lower than forecast in the Budget at $13.5 billion.
Radio New Zealand's political editor says the lower tax take helped push the deficit, excluding investment gains and losses, to $2.1 billion, $449 million above forecast.
When investment gains by the New Zealand Superannuation Fund and ACC are included, the operating balance recorded a surplus of $90 million in the three months to the end of September.
Net debt stood at $54.9 billion, or 27% of gross domestic product.
The Government expects to return to surplus in the June 2015 financial year but economists say that is unlikely, given a weak global recovery.
Finance Minister Bill English says the accounts confirm the Government is making progress, but it still needs to restrain spending for years to come.
Prime Minister John Key says it's touch and go as to whether the Government will reach its target of returning the books to surplus in 2014-15.