The company will be holding an annual general meeting later on Wednesday, where shareholders will vote on remuneration for senior bosses.
Persimmon's chief executive Jeff Fairburn has come under fire in recent months for a potential £100m payout as a result of an incentive plan voted on by shareholders in 2012.
The Church of England had also promised to vote against the company's remuneration report.
He is in line to pocket a near £75m payout, including a £25m share payout in the summer.
"And so please let me take this opportunity to apologise unreservedly to our shareholders".
"It is a matter of profound regret that we got to the position where we had a company with an exceptional management team, delivering exceptional, market-beating performance, that has been overshadowed by a row over pay".
The asset management arm of Standard Life Aberdeen owns 7.1 million shares in the United Kingdom housebuilder on behalf of its clients, representing a 2.3% stake.
Persimmon shareholders have given the housebuilder a bloody nose in a vote on the company's executive pay and bonus scheme.
"Company directors have a legal responsibility to act in the best long-term interests of the company that employs them".
The group said forward sales were around 8 per cent higher year on year at £2.76bn since January 1. The FTSE 100 company said that 9,048 homes had been forward-sold in the year to date, with an average selling price of £236,500 compared to £229,500 a year earlier.
Looking ahead, Persimmon's board said it remains confident of the future prospects of the Group.