A third of investors in Drax have voted against its remuneration report after its finance chief was awarded a bonus of almost £500,000.
Shareholder adviser Institutional Shareholder Services had recommended voting against the report.
It said that Will Gardiner's bonus was "excessive" given the power company's performance the previous year.
Underlying profits fell from £46m to £21m for 2016 and the dividend was slashed from 5.7p to 2.5p a share.
Chief executive Dorothy Thompson was awarded a dividend of just over £750,000, bringing her total pay for 2016 to nearly £1.6m - an increase of more than £300,000.
Mr Gardiner, who joined in late 2015 from semiconductor maker CSR, was paid a total of £971,000.
Drax said it would hold further talks with shareholders in the wake of the protest vote.
"Discussions have already taken place with a number of institutional shareholders who did not support the remuneration report or remuneration policy resolutions," the company said following the vote at its annual meeting.
Almost a quarter of shareholders voted against Drax's new remuneration policy, which will apply from this year.
The company's power station near Selby in north Yorkshire generates 7% of the UK's electricity.
Earlier this year, one of the City's top fund managers warned that executive pay was "too high" and that investors were ready to take stand with firms that awarded hefty rises to bosses.
David Cumming, head of equities at Standard Life, said his firm "could not justify" pay going any higher.
"We continue to see too many proposals that would bring a substantial increase [in pay], and we have to signal that we are not happy with that," he told the BBC.
Meanwhile, Blackrock, the giant American investment fund, has told the chairmen of the UK's biggest companies they must stop making big payments when executives leave, and in lieu of pensions.
It would only approve pay increases for directors if workers' wages also rose.
BlackRock is a major shareholder in almost every company listed on the FTSE 100 and FTSE 250.