The highest earner at the Wellcome Trust was paid more than £3.17m in the year to 30 September 2018, the latest accounts show.
The salary is the highest of the six members of the charity’s investment team who earned more than £1m for the year covered in the latest accounts, amid another year of strong investment returns at the charity.
The salary is lower than last year’s highest remuneration package, which was worth £3.7m, but this still makes the Wellcome Trust the highest-paying organisation in the charity sector, according to Third Sector’s research on senior executive pay.
The Wellcome Trust did not name the person who was paid £3.17m for the year covered by the accounts.
The accounts name three members of the charity’s investment executive team: Peter Pereira Gray, managing partner and chief executive officer for investments, Nicholas Moakes, chief investment officer, and Danny Truell, emeritus partner and former chief investment officer at the charity.
The accounts say that pay for senior staff in the charity’s investment team is performance-related. It includes unspecified long-term incentive plan payments reflecting returns over a three to five-year period and a bonus scheme based on "individual achievements".
In a statement, the Wellcome Trust said the decision to use an in-house investment team had saved the charity "hundreds of millions of pounds" in fees that would otherwise have been paid to external investment managers.
The statement said the investment team had delivered investment returns of £2.2bn in the year covered by the accounts and a 203 per cent increase in the charity’s investment portfolio since the 2008 financial crisis.
The accounts show that the charity’s investment portfolio grew by 10.7 per cent after inflation, with investment assets climbing from £23.2bn to almost £25.9bn.
Jeremy Farrar, director of the Wellcome Trust, said: "By paying our outstanding investment team in a way that is competitive for the sector and linked to portfolio performance, Wellcome gets better returns and has more to spend on our charitable mission of improving health."
The accounts show that overall income at the charity was £484.8m, compared with £425.3m the year before, and spending fell from £1.3bn to £781.2m.
Charitable spending fell from £1.2bn to £723m, the latest accounts show. The charity said this was because of "the timing of significant commitments", with no major renewals or large one-off awards in 2017/18.
Once net gains on the charity’s investment portfolio were included, the charity had a net increase in funds of £2.3bn.
Moakes said in a statement that, despite the strong returns over the past decade, the charity does not expect this to be repeated over the next 10 years.
"As the global economic cycle matures, markets have become more volatile," Moakes said.
"Our global focus and long-term horizon have helped us to navigate a choppier environment.
"We have therefore sharpened our focus on preserving liquidity and generating cash flow from the portfolio to support the mission."