In a statement, the tour operator said it recognised the “significant number of votes opposing the resolution.”
The concerns relate to various details surrounding bonuses and incentives, which are handed out to the senior management team.
"We acknowledge these concerns and plan to engage further with shareholders during 2016 on a number of matters as part of a planned review of our remuneration policy," Cook said.
"These matters include the use of holding periods, timing of disclosure of targets, shareholding guidelines and clawback."
Last year, chief executive Peter Fankhauser was handed a £4.3 million pay packet.
Former boss Harriet Green received more than £6 million, but a portion of this was handed to charity.
It is not the first time shareholders have given Cook a bloody nose over pay.
In 2013, just under 30% of shareholders voted against the remuneration report.
Cook defended its actions, which related to the incentives handed to Green and chief financial officer, Michael Healy, who remains at the company.
“The board’s guiding principle is to ensure that pay reflects performance, and that we do not pay for non-performance,” it said at the time.
While the resolution was passed, it is telling that so many investors decided to vote against it.