The operating balance excluding gains and losses (obegal) for the period was a $2.02 billion deficit against the Budget forecast on May 28 of $1.1 billion deficit.
The majority of the higher-than-forecast deficit was related to corporate tax revenue coming in $900,000 less than forecast.
Other individuals taxes revenue was $290 million, or 33.5%, lower due to higher refunds.
Lower-than-expected 2009 tax year profits, coupled with assumptions that changes to the provisional tax due dates would have on tax seasonal patterns that did not come about, made up the bulk of that figure, Treasury said.
However, better than expected investment returns reported by the New Zealand Superannuation Fund ($1.4 billion) and ACC ($700,000) offset the tax result, meaning the operating balance deficit was $175 million, better than the forecast of a $600 million deficit.
Polson Higgs taxation partner Michael Turner said the fall in tax revenue was not surprising, but there were several reasons for the drop.
There had been incentives for individual taxpayers to pay provisional tax on their previous year's income. As their profits fell, taxpayers were due for a refund.
For large companies, it had always been a difficult call on how to pay provisional tax. Until March, the penalty for underpayment of tax had been 14.24% interest. That had dropped to 9.73% in March, and fell again in June to 8.91%.
"With cash tight out there and given that going to the bank to get money to pay tax is not that easy, companies have become less concerned about paying the IRD interest."
While in the past large companies had paid the right amount of tax or a little bit more, now they were paying the right amount or a little bit less, he said.
Finance Minister Bill English said the statements confirmed it would take time for the economic recovery to flow through to the Crown's revenue.
"We are seeing some welcome early signs of New Zealand moving out of recession and expect this will see unemployment peaking next year lower and sooner than previously forecast."
Economists are forecasting unemployment to be 6.3% for the end of September when Statistics New Zealand releases its figures today.
Mr English said the road to recovery would be bumpy and that was reflected in the financial statements.
A clearer picture of the implications for the Crown accounts in 2010 was likely to emerge in the next few months when seasonal volatility in provisional tax was expected to have settled down.
"In any case, with the Government borrowing an average $250 million a week, every week, for the next four years, it's clear that the constraints imposed on the Crown accounts by the recession and its aftermath will be felt for some time to come," Mr English said.
An analysis of the Crown accounts showed that social security and welfare payments continued to dominate Government spending. In the three months to September, the Government spent $5.2 billion on social security and welfare, up slightly from the $5.1 billion forecast.
Health spending also increased in the quarter to $3.2 billion, and education spending increased 2.3% to $2.9 billion.
