As many as one in four Granada shareholders voted against senior management's pay packages and Allen's two-year rolling contract. One in 10 shareholders voted against his re-election as chairman of the company.
Shareholders are said to be concerned that the packages could be carried over to the merged ITV, which could then see management cash in on the merged company.
The shareholder unrest did not hit Granada shares, which were up 4.69% to 64.25p today while Carlton was up 3.12% to 99p.
Carlton, which holds its AGM next Tuesday, is expected to face similar unrest from its shareholders concerned about the remuneration packages of its management.
The news came as said that first-half advertising revenues will be flat as the situation in Iraq was causing some advertisers to defer spending into the later part of the year.
Allen said revenues had not been "as buoyant as in the first quarter" but, despite revenues slowing in the second quarter, April revenues looked set to rise 3%-5% on last year.
The overall slowdown in ad revenue was cushioned by a strong performance by its digital channel ITV2, which has seen ad revenues grow 300% on last year.
"Nonetheless, the combined national advertising revenue for ITV1 and ITV2 for the six months to March is expected to be up on last year. Granada's ITV1 revenue in the first half last year was £435m and we estimate that this year will be approximately the same. This is despite the important Easter advertising moving from the first half last year to the second half this year," Allen said.
Granada's merger with Carlton is currently in the throes of a competition inquiry. Allen said the regulatory process is "moving forward" and that he expects the Competition Commission to complete its report on June 25, running concurrently with the passage of the communications bill.
Allen added that Granada has been working hard to improve its schedule and that ITV1's primetime adult viewing share in all homes rose to 31.7% in the three months to December. This was up from 31.1% in the six months before.
In January and February, its share increased to 33.1%, "5.5 percentage points ahead of the BBC", he said.
Allen singled out 'The Royal', 'Coronation Street' and 'The Bill' as high ratings winners. He said that its Saturday evening show 'Ant & Dec's Saturday Night Takeaway' attracts up to 46% of 16- to 34-year-olds.
ITV1's impacts in the 16- to 34-year-old ABC audience were up by 16% in January and 12% in February compared with a year earlier. The channel also achieved a 44.6% share of adult commercial impacts, beating its target. ITV has just enjoyed a big hit with the fifth series of 'Cold Feet', with the final episode scoring more than 10.2m viewers.
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