NZTA's state highway manager Rod James told Radio New Zealand the figure was not out of the ordinary.
"It certainly is a lot of money, [but] it's certainly not out of context with other similar processes.
"In this region we've had three other boards of inquiry that have gone through in the past few years - Transmission Gully's one, MacKays Expressway, this one and the Peka Peka to Otaki section of the Kapiti Expressway - all of those have been similar kinds of ranges of costs.
"That's the kind of cost of going through a process like this."
The cost of staff attending the board of inquiry blew out after running 12 weeks longer than originally expected, Mr James said.
The agency had until Friday to appeal the decision, but had yet to confirm whether they will.
Wellington Central MP Grant Robertson told Radio New Zealand the $11 million had gone to waste.
"The NZTA didn't get those things right that the board of inquiry have highlighted, obviously money will always be spent in preparing a project like this, but ultimately all you have to do is listen to what the board of inquiry said to realise that money has definitely been wasted here."