The signing is part of an effort to stabilize relations just weeks before the inauguration of US President-elect Donald Trump, who has promised to slap huge tariffs on Chinese imports.
The agreement, which dates back to 1979, had been renewed every five years for decades, including during Trump's first term, until last year when diplomatic relations between the two countries were at record low.
Tensions soared that year over an alleged Chinese spy balloon that was shot down over US airspace, a meeting between Taiwan's president and the US speaker of the House, and American military aid for Taipei.
But the agreement was nonetheless extended twice by six months until renegotiations could start.
The protocol "has new provisions" including on data reciprocity, which resulted from months of negotiations, a US senior administration official told journalists on condition of anonymity.
The push to renew came even as the United States attempts to wean itself from its dependence on Chinese semiconductors and wages battle against state hackings by Beijing.
- Zones of cooperation -
According to the administration official, the new agreement strengthens provisions on safety and dispute resolution as well as contains provisions on protecting intellectual property.
It also contains an exit clause in the event of non-compliance, and excludes cooperation in the fields of sensitive or emerging technologies.
The United States restricts technology exports to China, particularly semiconductors as it attempts to strengthen its own domestic output.
Taken together the revisions "create the most robust" national security guard rails of any government-to-government scientific cooperation with China, the US official said.
In a report released in September, the House Select Committee on the Chinese Communist Party, which is controlled by Republicans, denounced what it said was a gradual leak of US know-how into China.
In the report, lawmakers stated that "hundreds of millions of dollars in US federal research funding over the last decade has contributed to China's technological advancements and military modernization."
While the United States and China are fiercely competitive, they have found reason to cooperate in several broad areas including scientific research, climate change and trafficking of fentanyl, the synthetic drug wreaking havoc in the United States.
Beijing and Washington have also reestablished direct military-to-military communication, which US President Joe Biden and his Chinese counterpart Xi Jinping supported during their last meeting on the sidelines of the APEC summit in Lima in mid-November.
Scientific cooperation "is part of the overall broader competitive relationship we have with the PRC," the US official said, using the acronym for the People's Republic of China.
"Within that relationship there is scope for limited cooperation in areas that advance US interests," the official said, such as oceanography, seismology, meteorology and even agriculture and health, including vaccines.
Trump has repeatedly claimed, without proof, that the Covid-19 pandemic originated from a virus that leaked from a Chinese laboratory, something Beijing firmly denies.
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