Mr Johnson said the new route, which opens on Sunday, honoured the “profound ties of history and friendship” between the UK and its former colony.
But Chinese foreign ministry spokesperson Zhao Lijian told reporters on Friday that China will no longer recognise the BNO passport as a travel document and proof of identity starting from January 31.
"The British side's attempt to turn a large number of Hong Kong people into second-class British citizens has completely changed the nature of the two sides' original understanding of BNO,” said Mr Lijian.
"This move seriously infringes on China's sovereignty, grossly interferes in Hong Kong affairs and China's internal affairs, and seriously violates international law and the basic norms of international relations.”
He said the Chinese government “reserves the right to take further measures”.
Under the UK’s plan, as many as 5.4 million Hong Kong residents could be eligible to live and work in the UK for five years before applying for citizenship.
Demand soared last year after Beijing imposed sweeping new national security laws on Hong Kong after months of pro-democracy protests.
The (BNO) status was created before the UK handed responsibility for Hong Kong back to China in 1997.
From Sunday, those eligible for a visa can apply online and will need to book an appointment to attend a visa application centre to provide their fingerprints.
Then, from February 23, (BNO) status holders who have an eligible biometric passport will be able to use an app to complete their application from home – the first time non-European Economic Area citizens have been able to do so.
UK Foreign Secretary Dominic Raab has said China’s imposition of the national security law in Hong Kong “constitutes a clear and serious breach of the Sino-British Joint Declaration contrary to international law”.
“We have been clear we won’t look the other way when it comes to Hong Kong. We will live up to our historic responsibility to its people,” said Mr Raab.
Additional reporting by PA Media.