At the group’s annual meeting on Friday, investors voted by almost 54% to reject the company’s remuneration report.
The revolt was a major setback for Kier’s board, but is only advisory and not binding.
At issue was the £2.6m annual package offered to chief executive Andrew Davies when he took up the job last April.
Rebel shareholders are understood to have been concerned with the £1.19m that could be paid to Davies under a long-term incentive scheme.
His package is a £595,000 base salary, annual bonus of up to 125% of salary and £45,000 in pension top-ups.
Kier’s remuneration report also revealed the company had footed the bill for former boss Haydn Mursell’s broadband subscription – deemed a work expense – for a further five months after he exited.
In a statement after the set-back, Kier said that it would continue to “reflect carefully’ on the points that investors had raised.
“The remuneration committee will engage further with the company’s shareholders and the proxy advisers to understand their views and to decide how to address them,” said Kier.
It added that the firm would publish an update within the next six months on the views it has received from shareholders and the actions it has taken, or proposes to take, in response.