Toyoda was facing shareholders for the first time since the Japanese automaker's reputation for quality was damaged by the recall crisis that started last October.
Again bowing deeply after the remark, Toyoda also said the company was doing its utmost to improve quality control and thanked shareholders for their support.
"I apologize deeply for the concerns we have caused," he said. "We believe our most important task is to regain customers' trust."
The meeting was closed to the media.
Toyota, the world's biggest automaker, has been working to patch up its reputation after more than 8 million vehicles were recalled worldwide over reports of unintended acceleration and other defects.
Although the recall debacle hung over the meeting, statements from Toyoda and other officials were met with polite applause. A handful of shareholders shouted their anger.
Toyota executive vice president Satoshi Ozawa said recall-related costs for the fiscal year ended March totaled $4 billion.
Toyoda said directors on the board will again forego bonus payments. There were no bonuses the previous year after Toyota reported the worst losses in its history as the financial crisis sent auto sales plunging.