Amnesty elected not to run the campaign because it was considered to be too "negative" and failed to get across its message on China. However TBWA\France entered it for the Cannes Lions advertising festival last month, where it won a bronze Lion.
The work, which combines Olympic imagery with graphic portrayals of people being tortured, has since been widely disseminated online and has been the subject of a backlash in China.
Unusually, the ads appeared with the web address www.amnesty.com, rather than the correct organisation website address www.amnesty.org.
Amnesty International's global HQ in London has disowned the print ads. A statement has been posted on its website homepage stating: "Amnesty International would like to make clear that it was not involved in the dissemination of a series of images that have been circulating on the web in relation to the Beijing Olympics."
An Amnesty UK spokesman said: "The ads were a response to a brief from Amnesty France, but they were rejected for being very negative and because they don't reflect our message on the Beijing Olympics.
"We are not opposed to China holding the Olympics. What we have been campaigning on since 2001 when China won their bid to host the 2008 games was to get them to honour their promises to improve human rights in China, which they haven't done.
"Amnesty has a global message on the Olympics but it is interpreted differently by different sections of Amnesty. It is just one of many campaigns."
Tom Carroll, TBWA\Worldwide chief executive, told The Wall Street Journal on Monday that the ads were the work of one individual in the Paris agency.
He said if the agency head office had known about the ads it would never have produced them or entered them into the Cannes show. Carroll said the agency was carrying out an investigation and would take "appropriate action" to ensure it didn't happen again.
TBWA\China, which has been working on an Olympics campaign for Adidas in China, has also distanced itself from the campaign.
A TBWA\China spokesperson told Media Asia that neither TBWA\International nor TBWA\China had involvement or prior knowledge of the development of the campaign.
"TBWA\International is a non-political organisation. Our offices in China have responsibly contributed to the development of China's advertising and marketing industry for more than 12 years.
"TBWA\China is proud that Beijing is hosting the Olympic Games in August and remains committed to supporting its success."
Chinese bloggers have called for a boycott of TBWA over the ads, while a Chinese government body, The China Society for Human Rights Studies, said the ads were an attempt to "smear" the country ahead of the games.
Last September, MUW Saatchi & Saatchi Slovakia produced a similarly graphic print ad campaign for Amnesty Slovakia highlighting human rights abuses in China ahead of the Olympics, under the strap line "China is getting ready".