The Treasury said that is because some Government departments spent more than had been expected over that period.
A spokesman for Robertson said the deficit was not unexpected. He said some spending from Government departments was deferred from before June 30, to after that date.
This meant that the surplus, as reported in the June financial statement, was higher than expected.
Robertson flagged this last month. He said Government spending was 1.4 per cent below forecasts as of June 2018 because of "timing issues".
This was largely a result of things like lower-than-expected spending across the education sector and less than had been forecast being spent on the year-end family tax credit claims, he said at the time.
As a result of this "timing issue" some Government department spending over the past four months was higher than the Treasury had expected over that period.
"The October accounts always have the greatest chance of the greatest variation from forecasts because they are the furthest away from the Budget forecasts," the spokesman said.
He added that the next set of Crown accounts will be compared against much more up-to-date forecasts, which will be contained in the Half Yearly Economic and Fiscal Update (HYEFU), next month.
Meanwhile, Robertson said in a statement the Crown accounts show New Zealand has a strong job market.
The growth in tax revenue, which at $26.1b, was $200m ahead of forecasts – "higher than forecast employment growth" was cited as a reason for this growth.
Last month, the unemployment rate dropped to 3.9 per cent – a 10-year low.
"Net debt at the end of October was 21.1 per cent of GDP, versus the Budget 2018 forecast of 21.6 per cent."
Even National's Finance spokeswoman Amy Adams admitted the books were in good shape.
But she said that is largely down to the policies of the previous National government.
"While New Zealanders are struggling with a rising cost of living, the Crown accounts show the Government is collecting more tax while at the same time undertaking large and untargeted spending schemes which have come in above forecast.
"This means New Zealand is more vulnerable should economic growth continue to slow as many commentators are predicting and business confidence surveys continue to point toward."