The charity is refusing to name the employee, but claims it is not chief executive Tony Hall. The salary the person earns is twice that received by any local government chief executive.
During 2003/04 the Opera House got £21.7m or 82 per cent of its voluntary income from the National Lottery.
"It's a board directive not to reveal the names behind the salaries," said Chris Millard, the opera's director of press and communications.
Debra Allcock Tyler, chief executive of the Directory of Social Change, said she was "shocked" by the amount.
"I don't think it reflects well on the sector," she said. "There is nothing wrong with chief executives earning a good wage but anything in excess of £150,000 to £200,000 sends out the wrong message."
The finding is contained in the 2005 Charity Trends survey, which the Charities Aid Foundation publishes tomorrow.
The International Planned Parenthood Federation, the Institution of Electrical Engineers and the National Trust were the only other charities to award £200,000-plus salaries.
"Some charity salaries are beginning to compare favourably with the private sector," said Richard Evans, chief executive of headhunters CF Appointments.
- See News in Focus, page 20.