"We ended up going down the middle and that's now fixed."
That increase was roughly $330,000 on turnover of about $3.3 billion, Mr Whelan said.
"Obviously universities are under huge financial pressure and we begrudge paying anything which doesn't add significant value."
An Auckland University spokeswoman said the cost would not be passed onto the students because there was legislation that set how much students paid in fees.
A technical aspect of the issue went through the court system and a ruling from the Court of Appeal was released today.
It said the universities found the price increase by CLL "unacceptable".
"They pointed to declining demand, the result of digital media supplanting photocopied materials."
The universities wanted the licences to be declared a set of licences, while CLL wanted them declared a scheme, the Court of Appeal ruling said.
If the licences could be declared a scheme, they could be altered collectively, while a set of licences would need to be individually altered.
The Copyright Tribunal agreed with CLL and ordered they be declared a scheme, but the High Court reversed that decision.
The Court of Appeal has now reversed the High Court decision and again ruled the licences a scheme.
Mr Whelan said the ruling created a principle that universities would not be able to negotiate costs in 2017 when the next negotiations take place.
The universities' lawyer John Katz said it was too early to know if an appeal on the ruling would be lodged.