Thomas Cook has declined to comment on a report identifying it as paying an unusually high salary to chief executive Manny Fontenla-Novoa.

The report by Meis Executive Compensation Data suggests Thomas Cook paid Fontenla-Novoa at least £200,000 more last year than would be expected of a company with its stock market value.

Fontenla-Novoa earned a salary of £850,000 last year. Thomas Cook was the only travel and tourism company in a group identified by Meis as paying well above the going rate.

Meis is part of the Inbucon group which provides pay reports to institutional investors such as pension companies. It calculates the rate of chief executive pay investors might expect given a company’s turnover and market capitalisation. Thomas Cook is largely owned by such investors, with AXA insurance and Lloyds Banking Group its two largest shareholders.

Inbucon managing director David Brooks told Travel Weekly: “If a company is paying a lot more, there might be good reasons for this – or it could be the company is just paying a heck of a lot. Cook is paying over £200,000 more than would be expected. There would need to be a reason for that.”

He said: “We steer clear of making value judgments. But there seems to be a relation between good returns to shareholders and a reasonable and clear remuneration package for chief executives.

“Getting the base pay right is the first step to getting [chief executive] bonuses right. Bonus payments, share incentives and pensions contributions are all normally a percentage of base pay.”

Fontenla-Novoa’s basic salary was swelled by bonuses and benefits to a total pay package of £2,272,000 last year, putting him on a par with the 25 highest-paid bosses in the FTSE 100.

However, Thomas Cook dropped out of the FTSE 100 last summer and by yesterday had lost almost 30% of its share value since March 2010 – most of it in a precipitous decline last May following the volcanic ash cloud.

Thomas Cook would not comment on the report. But the chief executive’s salary will have been set when the group was a member of the FTSE 100, for which Meis identified the median base pay for someone in his position as £800,000. His salary will also have been linked to that of Tui Travel chief executive Peter Long, who likewise was paid a basic salary of £850,000 in 2010 and enjoyed total payments, excluding pension, of £2,066,000.

Tui Travel remains a member of the FTSE 100 but has lost 20% of its value over the past 12 months – most of it also last May – while the FTSE 100 has risen 2.66% over the period.