Shareholders' anger focused on Flynn's two-year rolling contract, which last year saw him pick up £1.2m after a 40% pay hike. He is also in line to receive a whopping pay-off, running to two years' salary plus hefty bonuses.
The two-year contract goes against the 12-month maximum now being called for by shareholder groups under new attitudes towards corporate governance.
The vote at the AGM saw shareholders reject the Remuneration Report by 376,922,138 to 364,776,806, with 24,421,396 abstentions.
The National Association of Pension Funds urged its members to vote against the remuneration report rather than simply abstaining. It said the vote demonstrated the ongoing concerns of shareholders over executive pay and bonuses.
The defeat follows trouble earlier this year for Sir Martin Sorrell, the WPP Group chief executive. After some shareholder disquiet, a controversial executive pay plan, which could see Sir Martin receive a £44m bonus, was cleared by shareholders.
In a statement, Aegis, the owner of the Carat and Vizeum media networks, said that the board "clearly registers shareholders' particular sensitivity to contractual notice periods and payments on termination".
Aegis said that it would continue its dialogue with shareholders in light of the vote and will discuss the appropriate steps that need to be taken.
Trouble at the Aegis AGM followed the company announcing that group revenues were up by nearly 11% for the first quarter of the year.
Aegis shares continued to gain ground this morning, rising 1.1% to 89p. Yesterday, they were trading up 4.2% at 87p.
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