China's access to large amounts of genetic data, giving it insight into population traits, could push it towards increased economic and military domination.
Experts warn it could help China gain a monopoly over pharmaceuticals, lead to soldiers being genetically enhanced, and result in the engineering of pathogens to be used as weapons of war.
So far, 8.4 million women have taken BGI's test, branded as NIFTY, worldwide. It is among the world's top-selling non-invasive prenatal tests (NIPT) and is sold in 52 countries, including New Zealand.
Other NIPT companies also reuse data collected during testing for research. Scientists and ethicists have said the scale of BGI's operations and its links to the military are concerning.
Antenatal Results and Choices, a British charity for parents, said mothers-to-be would be "horrified" to think their data could be used for nefarious purposes.
"This is concerning," said a spokesman. "When women sign a consent form for use of their data after a prenatal test, their expectation is that such use will be within legitimate and ethically sound clinical research. Most would be horrified if it was being used for politically motivated or even military purposes."
BGI has produced millions of diagnostic tests for export, including for coronavirus and Ebola. It has been involved with the Human Genome Project since 1999.
It began working with military hospitals to study the genomes of foetuses in 2010 and has published joint studies with PLA researchers to trial and improve its tests. There is no evidence that BGI has violated privacy agreements or regulations.
The company said it obtained signed consent and destroyed overseas samples and data after five years, adding: "At no stage throughout the testing or research process does BGI have access to any identifiable personal data."
It "has never been asked to provide - nor provided - data from its NIFTY tests to Chinese authorities for national security or national defence purposes".