Xie Zhenhua, director of the State Environmental Protection Agency since 1993, resigned on Friday and was replaced by the former forestry director Zhou Shengxian, Xinhua news agency said, citing a statement by the country's cabinet.
State television said Xie had resigned due the administration's failure to address the crisis. The State Council, or cabinet, and Communist party had approved his resignation.
China Central Television said the administration, as the main body for environmental protection, had not paid enough attention and fell short in evaluating the possibly severe results of the incident.
"It holds the responsibility for the losses," it said.
The high-level reshuffle follows mounting criticism over the government's handling of the spill. Most of the criticism has been aimed at officials in Jilin province where a blast at a chemical plant poured 100 tons of cancer-causing benzene into the Songhua river on 13 November. Officials failed to report the spill.
The move is also in line with a campaign by President Hu Jintao to instil official accountability at the highest levels of government, dating back to the sacking of the health minister and Beijing mayor after a cover-up of the deadly outbreak of Severe Acute Respiratory Syndrome (Sars) in 2003.
The environmental protection administration said that from 14 November to 17 November it received no reports from the Jilin authorities, meaning the best opportunity to control the spill was lost.
The China Daily newspaper quoted Wang Yuqing, Administration Vice-Minister, as telling a national teleconference: "A reckless pursuit of economic growth and a lack of emergency response mechanisms have seen China experiencing a high rate of environmental disasters."
The toxic slick forced officials in Harbin, a city of 9 million people downstream from Jilin in Heilongjiang province, to shut off its water for five days. The slick passed the city on Sunday and is making its way through Heilongjiang towards the Russian border.
Caijing Magazine noted in a commentary that Beijing officially notified Moscow of the problem only on 22 November.
The publication said that Xie had contended that the toxic chemicals were becoming diluted as they were carried down the river, so 22 November was not too late to inform the Russian authorities.
"In the realm of foreign relations, however, such an explanation does not go over too well"
"In the realm of foreign relations, however, such an explanation does not go over too well," it said.
The slick was winding its way northeast towards the Siberian city of Khabarovsk, through areas populated by millions of Chinese, and on Friday it was passing through the town of Dalianhe, where water supplies were cut off on Thursday.
The community of 67,000 was relying on wells and tapping into supplies from neighbouring communities, a town official said. Schools were closed and classes were unlikely to resume until next Tuesday, when the pollutants were due to have passed, a teacher said.
Downstream in Jiamusi city, officials shut down a major water plant near the river serving 2.4 million people to prevent contamination. They were tapping groundwater and deepening wells before the pollution's expected arrival on Tuesday, Xinhua reported.
Cold weather is freezing the Songhua, slowing the slick down, it said.
Freezing conditions are slowing
the passage of the benzene
Wang said 36 major pollution accidents had been reported by the end of November, warning there could be more that have gone unreported.
Regional governments were giving tacit consent to discharges of pollutants into rivers and some had approved polluting businesses that the central government had banned, he added.
"Local environmental protection bureaus need to increase their ability and improve their equipment to supervise and handle pollution," he said.