The extra rights for investors, granting them a binding vote on future pay and a single figure for each director's pay packet, came into effect in October 2013 with the aim of aligning the company's goals with the interests of shareholders.
With most of this year's annual meetings now complete, the average FTSE 100 company has seen 8.9 per cent of its investors vote against future pay or abstain from the vote. The level of dissent rose to 9.88 per cent when investors voted on the previous year's pay, according to figures from Manifest, the proxy voting agency.
Both figures are slightly higher than the 2013 average of 8.13 per cent dissent against pay for the prior year, which was the only vote available before the rules changed.
The percentages are influenced by a handful of large rebellions, and more investors joined in with the biggest dissents than a year ago.
Figures from KPMG earlier this month showed that 12 per cent of listed companies have this year endured "significant" shareholder rebellion, which is classed as more than a fifth of investors voting against pay. This compares to just 2.5 per cent in 2013.
The revolts are not as widespread as they were during the so-called shareholder spring of 2012, when corporate giants including WPP, Aviva and Barclays endured particularly heavy criticism and the average level of investor dissent on pay votes rose to 11.7 per cent.
However, influential shareholders have been quick to raise concerns about specific problems this year, including fund manager Fidelity, which pledged to vote down any policy that allowed directors to cash in long-term share awards after just three years.
Standard Life Investments, meanwhile, has taken to voting against the reappointment of individual board members to reinforce its disapproval of pay awards at firms including BG Group, Aberdeen Asset Management and BSkyB.
"I think there's an informal sense that if 10 per cent or more of your shareholders are voting against you as a person, you have got to sit up and take notice," said Jonathan Cobb, governance and stewardship director.
The largest blue chip shareholder revolt to emerge from the new pay policy votes was Standard Chartered in May, when 41 per cent of investors rejected the bank's remuneration plans for the next three years.
While it was not enough to defeat the policy altogether, shareholders highlighted concerns about a proposal to reward top staff based on annual targets rather than more long-term goals.
Burberry, which shares its chairman Sir John Peace with Standard Chartered, has stood by its plan to hand up to £10 million a year to new chief executive Christopher Bailey, despite 52 per cent of its shareholders refusing to support the package when they voted in July.
At FTSE-250-listed FirstGroup, more than a quarter of the company's investors voted against last year's pay, which included almost £2m for chief executive Tim O'Toole.
While the rebellion was slightly smaller than in 2013, when 29 per cent of the transport company's investors voted down the remuneration report, it was enough to prompt chairman John McFarlane into promising a "deep review" of executive pay.
A handful of shareholder meetings, including that of drinks group Diageo, are due to take place in the next few weeks.
The new rules on executive remuneration at UK-listed companies were introduced last October in response to a report by economist John Kay, which encouraged stock market participants to act as long-term stewards of companies rather than focus on short-term gains.
The EU intends to adopt similar rules on pay votes for the 10,000 firms that are listed on stock exchanges across Europe.
Other reforms to emerge from the Kay report include plans to end mandatory quarterly reporting and the launch of the Investor Forum, which will hold its first meeting of major shareholders next month.