"The Chancellor rejects the accusation very clearly," her office said in a statement sent to the German Tagesspiegel daily.
The weekly Die Zeit and Sueddeutsche Zeitung daily had reported that Germany's Federal Intelligence Service, the BND, had in 2020 judged the probability of a Wuhan lab leak being responsible for the pandemic to be between 80 and 95 percent.
Having commissioned an investigation, Merkel then prevented the results from being published, the newspapers reported, as did her successor, the current Chancellor Olaf Scholz, who took office in December 2021.
The authorities were reportedly keen to avoid sowing panic amongst the population and also feared stoking a diplomatic crisis with Beijing.
Merkel refused to be drawn on the detail of the allegations and directed enquiries to the current chancellery, which keeps government archives.
Jens Spahn, who was Germany's health minister at the height of the pandemic, denied knowledge of the findings.
"I've only heard about it through the media," he said on the RTL-Germany television channel.
He added that the lab-leak theory had long been considered a possibility and that confirming or denying it would anyway have had no bearing on the public health measures taken.
"The virus was what it was and caused the damage that it did, as we know," he said.
Whether the virus which causes Covid accidentally escaped from a laboratory or spread from an animal to humans remains a matter of debate.
Part of the scientific community believes it was more probable that the virus spread to humans via an animal that had likely itself been infected by a bat.
Some agencies in the United States, such as the FBI and the Department of Energy, have said they lean more towards the lab-leak theory, with varying degrees of confidence.
Asked about the allegations in the German press, the Chinese Foreign Ministry said Thursday that scientists should be the ones to research where the virus came from.
"This issue should be addressed in a scientific spirit," its spokeswoman, Mao Ning said.
She added that a joint report by experts from the World Health Organization (WHO) and Chinese scientists four years ago judged the lab-leak theory to be "extremely unlikely."
Germany's 2020 investigation relied in large part upon data gathered in China, Die Zeit reported, including unpublished doctorates carried out in Wuhan that looked at the impact of coronaviruses on the human brain.
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