It comes at a time when fears are worsening that Hong Kong's freedoms are under threat from an increasingly assertive Beijing.
There are already concerns that Chinese operatives are working undercover after the alleged abductions of a city bookseller and a reclusive mainland businessman.
The high-speed rail line between Hong Kong and the southern Chinese city of Guangzhou, 80 miles away, is due to open in 2018.
Its Hong Kong terminus will be in the heart of the semi- autonomous city, on its famous harbourfront, not near the boundary with China that lies further north.
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Critics say the plan is a clear breach of the city's mini-constitution, the Basic Law, which guarantees freedoms unseen on the mainland and prohibits its law enforcers operating in Hong Kong.
Justice secretary Rimsky Yuen stoked opponents by likening the arrangement to the relationship between a landlord and tenant.
"The landlord has rented a house to me and then realised he didn't have enough space and asks me, can you rent a room to me? He has that right," he said on a radio talk show yesterday.
"If China is our landlord, that means they could ask us to give back land any time," opposition lawmaker Tanya Chan told AFP today.
Barrister and former lawmaker Margaret Ng said there was no legal basis for the move to create what the government is calling a "mainland port area" on Hong Kong soil.
The territory's boundaries are protected by its constitution, she said.
"If you choose to carve out part of it and call it something else, then we lose our protection altogether," said Ng.
There are already transport connections between Hong Kong and the mainland, but Chinese immigration checks are done on the other side of the border.
Yuen said the arrangement would not diminish the rights of Hong Kong people, who are used to freedom of expression and accessing social media sites like Facebook, which are banned in China.
But when asked by reporters whether passengers would need to change their behaviour in mainland parts of the station, Yuen said they would be treated as if they had crossed into China at any other Hong Kong border point.
The new high-speed rail line is one of a number of cross-border infrastructure projects which have increased concern that Hong Kong is being swallowed up by the mainland.