The April outbreak has been blamed on human error
One person was killed during the April outbreak, which came a year after Sars killed nearly 800 people worldwide.
The resignation is being seen as part of a push for greater accountability.
China's leaders want its bureaucracy, better known for high-handedness and widespread corruption, to be seen to respond to public criticism.
The official Xinhua news agency said Li Liming, director of the Chinese Centre for Disease Control and Prevention, had resigned for "mismanagement of the Sars virus" at the nation's most important infectious disease laboratory.
"Poor management of the virus triggered the Sars outbreak," Xinhua said, quoting sources at the health ministry.
Four other officials were disciplined, Xinhua added.
The BBC's Louisa Lim in Beijing says the case is the latest in a series of resignations by officials held responsible for disasters that could have been prevented.
Mr Li's resignation follows the publication of a government report on the outbreak.
China's media said the outbreak might have been triggered by scientists at the National Institute of Virology in Beijing experimenting inside the institute's laboratory.
Parts of the institute and laboratory could have become contaminated, which would explain why people whose work did not involve handling the virus became infected, the Beijing News said.
The  Chinese Government has announced plans to impose fines of over US$12,000 on media outlets if they report domestic disasters without permission. 

Two years in the planning, the law is expected to be in force by the end of the year and would affect reporting of natural and industrial disasters or anything that could “jeopardize the handling of emergencies,” or threaten social order. 

In a country which is infamous for its censorship there’s been outcry from press freedom campaign groups, but the Chinese government insist that the laws are primarily to give local governments more control in releasing information to the public. A government spokesperson said: "Journalists and media organisations have worked very hard to contribute to covering emergencies but I must say that some individual journalists have filed wrong reports or even fabricated facts."

Chinese journalists on the mainland  Hong Kong have criticised the law, calling it a “step backward.” The Xin Kuaibao (New Express) said it was concerned that local government would control information saying “there is no way of verifying that the information in the hands of the government is the truest and most accurate.”   

The  Committee to Protect Journalists (CPJ) meanwhile has expressed its concern. "The media have an important and potentially life-saving role in reporting health crises, natural disasters and other incidents of public concern that officials often have an interest in concealing," CPJ director Ann Cooper said last week. 

The proposed law is a worry for some in light of the Chinese government’s handling of previous disasters that were widely criticised. In 2004 several officials resigned for their handling of the  SARS outbreak, after public pressure sparked by domestic media. 

According to the Committee for the Protection of Journalists,  China imprisons more journalists than any other country, including two from the Southern Metropolis News for their reportage of the SARS crisis.