Shareholders applauded a succession of speakers criticising its remuneration policy while the head of the bank's remuneration committee, Sir John Sunderland, was heckled, and a major investment fund said it would not back the pay measures.
Barclays recently defied calls for restraint by hiking its staff bonus pool by 10% to £2.38 billion despite profits falling by a third and plans to cut thousands of jobs.
Chairman Sir David Walker defended the pay policy, saying Barclays had to act after it faced a drain on investment bankers to US rivals last year.
But there was applause when one shareholder, Phil Clarke, questioned whether nearly 500 staff being paid £1 million were worth it - and suggested halving their packages in order to increase dividends by 50%.
Mr Clarke said the performance of Barclays shares suggested the market did not have confidence in the highly-paid employees.
He said: "We are paying for Manchester United but we are getting Colchester United."