Robert Bauman, chief executive of SmithKline Beecham, was knocked out of the number one slot despite an 8.3 per cent pay increase that took his total to pounds 1.33m.
A survey of top directors' pay by Pensions Investment Research Consultants, an independent agency, also shows that two other businessmen, Sir Ian MacLaurin of Tesco and Richard Giordano of the BOC group, were paid more than pounds 1m.
The survey concludes that increases in pay were on average more modest than might have been expected in the light of the controversy surrounding the issue.
National Power caused a storm when it said that John Baker, its chief executive, saw his total pay increase by 160 per cent to pounds 383,935, representing the largest single rise. But this was less than the pounds 398,667 average payment to highest-paid directors in FT-SE 100 firms, the figures show.
In the latest financial year the average total board remuneration in FT-SE 100 companies increased by 1.4 per cent to pounds 2.32m. One-third of companies surveyed did not increase payments to the board.
Variations between companies are enormous, with companies including BAT and Tesco reducing total payments to the board as a whole while Argyll increased the payout by 88 per cent.
In a separate survey on political donations, the consultants say that United Biscuits is still the largest contributor to Conservative Party funds, giving pounds 130,000 in the latest financial year. Rothmans became joint number two with Hanson and P&O, each giving pounds 100,000. Rothmans previously gave to the Health Promotion Trust, a tobacco industry-funded organisation.
The consultants say that two FT-SE companies making political donations for the first time were Vodafone and Thames Water, the only privatised water or electricity company to do so. Both companies gave pounds 50,000 to Conservative funds.
Marks and Spencer gave pounds 50,000 directly to the party's coffers, having in the past contributed through British United Industrialists. M&S also gave pounds 10,000 to the Liberal Democrats, the only one of the top 100 companies to contribute to that party.
Among FT-SE 100 members more than a dozen companies increased political contributions last year while five cut back and two - British Airways and Rolls-Royce - stopped donations completely.