WHO head Dr Tedros Adhanom Ghebreyesus called on China to be more co-operative about the early stages of the outbreak, including with audits of laboratories.
Zeng Yixin, deputy health minister, said it showed "disrespect for common sense and arrogance towards science".
He said the plan was politicised and that China could not accept it.
The WHO was only able to send a team of experts to Wuhan - the city where the virus was first detected in December 2019 - in January this year.
Their investigators concluded that it was highly unlikely that coronavirus escaped from a laboratory, but the theory has persisted.
Earlier this month, Dr Tedros outlined the terms of a proposed second phase of the WHO investigation, including audits of science research institutions in the area where the virus was first identified.
He urged Beijing to "be transparent, to be open and co-operate" with investigators and provide raw patient data that had not been shared during the first probe.
Speaking at a press conference on Thursday, Mr Zeng said he was extremely surprised by the WHO proposal because it focused on alleged violations of China's laboratory protocols.
He said it was "impossible" for China to accept the terms, adding that the country had submitted its own origins-tracing recommendations.
"We hope the WHO would seriously review the considerations and suggestions made by Chinese experts and truly treat the origin tracing of the Covid-19 virus as a scientific matter, and get rid of political interference," Reuters quoted Mr Zeng as saying.
Yuan Zhiming, director of the National Biosafety Laboratory at the Wuhan Institute of Virology, also appeared at the press conference. He said the virus was of natural origin and maintained no virus leak or staff infections had occurred at the facility since it opened in 2018.
More than four million people have died worldwide since the start of the pandemic and the WHO has faced growing international pressure to further investigate the origins of the virus.
Earlier this year, US President Joe Biden also ordered American intelligence officials to "redouble" their own investigative efforts into the pandemic.
