The directors’ pay plan, or remuneration report (DRR), was rejected by 70% of proxy shareholders who voted at the company’s annual general meeting.
However, the vote is non-binding on the board, the company said.
Investor advisory firms ISS and Glass Lewis had both suggested shareholders vote against the remuneration report, partly because newly-appointed chief executive Rico Back is set to receive an annual salary of £640,000.
Mr Back’s pay comes in at £100,000 higher than that of his predecessor, Moya Greene who is retiring after eight years in the role.
But Royal Mail chairman Peter Long said that differences in pension arrangements meant that Mr Back’s “fixed pay” will be “exactly the same” as Ms Greene’s.
Responding to the vote, the board said it would consult further as it reviews its pay policy later this year.
The board’s remuneration committee chairwoman Orna Ni-Chionna said: “We are very disappointed that the advisory vote on the DRR was not carried.
“We have worked hard since becoming a public company to take a highly responsible approach to executive pay and have enjoyed strong support from our shareholders on all remuneration matters until this vote.
“We recognise and understand the reasons why our shareholders felt they could not vote in favour of the DRR this year.
“We will consult very closely with them and with the shareholder representative bodies as part of our scheduled review of the company’s remuneration policy. This is due to take place in the autumn.”
She added that shareholders had been told that the incoming chief executive’s pension entitlement was lower and the salary higher than the retiring chief executive.
“We did not feel it was appropriate to reduce the fixed pay for this very demanding role,” she said.
“Any potential increase in Rico Back’s variable pay is subject to meeting stringent performance conditions.”
Mr Back was appointed to the role of Group CEO and director in June after heading up Royal Mail’s European subsidiary GLS.
He has decided to stay in Zurich, Switzerland, from where he will commute to work at Royal Mail’s London headquarters.
Royal Mail stressed that, despite Mr back living in Zurich, he will pay full UK tax on all of his earnings, including bonus payments.