"We had to adapt to a new style," he told the committee.
"It's good to have a demanding Minister of Defence. I know we didn't meet his expectations but there was a period when we both had to get used to working with each other.
The minister had criticised the "quality and timeliness" of officials' advice, Mr Short said, but this had now improved.
Speaking to reporters afterwards, Mr Short said Mr Brownlee had criticised officials for not getting advice to him quickly enough, but stopped short of describing him as impatient.
"He just had different timelines," he said.
There were also misunderstandings between officials and the minister's office, over such things as whether to provide advice on Powerpoint or on A3 paper.
"It was a case of, he would tell us, and we were misinterpreting."
Defence bosses were also asked by the committee about the conditions Iraqi soldiers were living in at Camp Taji, where New Zealand's non-combat deployment is based.
Mr Goff cited a report by the US Defence Department which revealed in September that local troops at the base outside Baghdad did not have running water or power.
"We're trying to train people who are living in absolutely substandard, primitive conditions," he said.
Mr Short said this was the result of limited funding, which had been affected by corruption on the Iraqi side. New Zealand was unable to improve their situation, and it was up to the Iraqis to make changes, he said.
"We can't influence the Iraqi forces. We try to, but we can't actually change those conditions. It is their camp."
New Zealand soldiers had reported good morale and high engagement among the Iraqi forces they were training, despite their poor conditions.
If their performance or morale changed, New Zealand would raise the issue with the Iraqi Government.
Mr Short said New Zealand soldiers had access to running water and electricity, though they faced some hardship because they wore full kit and carried weaponry in 40C conditions.
