The London-based bank said its remuneration policy for directors was approved, but 40.8 percent of votes cast were opposed to the remuneration policy for its directors.
Several investors have criticised the introduction of more fixed pay based on short-term targets as the bank has sought to mitigate a European Union bonus cap. Some advisory groups said shareholders should oppose the vote on directors' pay as they want rewards based on more long-term measures.
Standard Chartered said it was "concerned that a significant minority of shareholders" voted against its new pay plan.
"We acknowledge their views, will reflect on them, and continue our dialogue with our shareholders and the governance bodies in order to address them properly," a spokesman said.
In a separate vote at the firm's annual shareholder meeting, investors approved the bank's plan to pay staff bonuses of up to twice their fixed salary this year.
The bank, which earns about four-fifths of its income from Asia, earlier on Thursday said a weak first-quarter conditions had continued in April and so far in May.
StanChart, which does not publish full quarterly results, said its first-quarter operating profit was down 6-9 percent from a year ago and revenue was down by less than 5 percent, broadly in line with analyst expectations.
Revenues in its financial markets division fell 16 percent after a slowdown in trading of interest rate products in particular, which has been seen across investment banks.
StanChart last year reported its first drop in annual profit for a decade and said the first half of 2014 would be difficult due to losses in South Korea and slowing growth in Asia.
The bank may not see a recovery in earnings until mid-2015, later than anticipated by investors, as potential economic headwinds in its two key markets of Hong Kong and Singapore could add to the bank's problems in South Korea and India, according to Chirantan Barua, analyst at Bernstein, who has an "underperform" rating on the stock.
"Pack that in with a challenging and uncertain capital regime that won't be resolved till the end of the year and you have a great deal of uncertainly around the stock," he said, referring to regulations requiring banks to strengthen their defences against potential financial crises.
The bank's London-listed shares closed up 2 percent, in line with a strong European bank sector.
END TO BOOM
StanChart's slowdown after a bumper decade has prompted Chief Executive Peter Sands to restructure the bank, and a management reshuffle last year saw the surprise exit of Finance Director Richard Meddings, once seen as a successor-in-waiting, and the elevation of Mike Rees to Sands' deputy.
Meddings is due to leave by the end of June, and a replacement as finance director has not yet been announced.
Sands combined the bank's wholesale and consumer banking units from April in an effort to combat the slowdown in its earnings growth by streamlining the business.
He is attempting to cut costs, and the bank said expenses in the first quarter were flat from a year ago.
"We are holding costs flat this year and are managing costs tightly," Meddings told reporters on a conference call.
He said the bank had slightly increased its number of staff in the first quarter.
South Korea remains a problem area and the bank is pruning its business there. Revenues in Korea fell by $110 million in the first quarter from last year.
StanChart has been struggling for years in South Korea amid weak returns, a dispute with staff, tough regulations and a rise in bad debts, and it wrote down the value of the business by $1 billion last year.
Weakness in Asian currencies, notably the Indian rupee and Indonesia rupiah, dragged on results as the bank reports in U.S. dollars. It said margins were also depressed.
Operating profit at the bank's wholesale business, which includes investment banking activities and contributes the bulk of group profits, was down about 5 percent from last year, while the decline in consumer banking was 15-19 percent.
Rival HSBC reported a 20 percent drop in first-quarter profit on Wednesday as revenue dropped in Brazil and at its investment bank, while last year's earnings were swelled by asset sales.
StanChart also said it expects to pay $350 million under a UK bank tax this year, up by a third from $266 million in 2013.