Eight companies had less than 75% shareholder support for their remuneration reports, and two reached less than 50%. That is a higher proportion than during the 'shareholder spring' of 2012, Deloitte said.
Only 26% of companies had their remuneration report supported by 95% or more of shareholders. Last year that figure was 53%, Deloitte said.
Actual bonus payments for 2015 performance rose, reaching 77% of the possible maximum compared to 73% for 2014. Only four companies paid no bonus, while four paid the maximum possible.
Stephen Cahill, a partner in Deloitte's remuneration team, said that the 2016 AGM season had been "bruising" for a number of companies, "perhaps even more so than … 2012".
While this only affected a relatively small number of companies, it is a cause for concern, Cahill said.
Shareholders are concerned about a lack of bonus target disclosure, and a lack of transparency in the link between executive pay and the performance of the business, Deloitte said.
Executive remuneration expert Lynette Jacobs of Pinsent Masons, the law firm behind Out-Law.com, said: "Shareholders' main concerns seem to relate to the high level and rate of inflation of total executive pay, and the growing contrasts between that and the income of both the shareholders and the general working population. In that context, bonuses appear to be the main driver of growing executive reward at present."
The median salary increase for executives remained at around 2%, as it has since 2012, Deloitte said. The median for annual bonus potential and potential long term incentive plans have remained steady, meaning that total pay has remained "broadly flat", Deloitte said
Deloitte's annual guide to directors' remuneration at FTSE 100 companies is due to be published at the end of this month, it said. The report is based on reports from two voting services.
Employee incentive plan expert Suzannah Crookes, also of Pinsent Masons, said: "The information published by Deloitte reinforces some of the messages that institutional investors and other commentators have been giving over the past few months, including that transparent disclosure and alignment between strategy, performance and incentives are fundamental to effective executive remuneration. Notably, this was an important aspect of the final report of the independent Executive Remuneration Working Group established by the Investment Association (IA), which is likely to influence imminent changes to the IA's influential principles of remuneration."
Remuneration committees need to ensure that executive pay is considered in the context of the rest of the company and seen to be fair and equitable with general employee policies, Deloitte said.
Cahill said: "We agree with the concept of the employee’s voice being heard by the remuneration committee. This could be achieved by the introduction of an internal employee forum which the remuneration committee would be required to consult with on a regular basis. Having to explain differences in policies and payments to a group of employee representatives would bring another dimension to remuneration committee discussions."
"Greater sharing of success may also be a helpful way to deal with the issue of inequality and we hope the government will look at this and consider ways in which companies can be encouraged to share a proportion of their profits with their employees," he said.
Crookes said: "This resonates with announcements made by the new prime minister that employee and also potentially consumer representatives may have a greater role to play in discussions around executive pay. We expect to hear more about this before Christmas, based on the prime minister's comments to the press at the G20 Hangzhou summit."
Cahill proposed that the annual vote on remuneration could be made binding.
"A vote against remuneration which has already been paid would cause some practical issues and we have concerns that this may actually make some shareholders even more reluctant to vote against. An alternative might be to introduce a ‘yellow card’ approach; for example if a company received less than 75% of votes in support [then] a binding vote would be required in the following year, giving the company time to address the problem," he said.
The prime minister has already announced that this will be considered, said Crookes.
"Fidelity Investments also indicated support for an annual binding vote, but on the basis that it would be forward-looking only, given the difficulties in having a binding vote in relation to payments already made and/or contractual arrangements already agreed," she said.
"We await publication of the full report by Deloitte at this end of this month which, as well as giving an interesting round-up of 2016, may indicate some trends and factors which will form part of the debate going into 2017," Crookes said.