More than 100 people have now died in China, with confirmed infections surging to more than 4,500.
High-speed trains and ferries that cross the border will be suspended from Thursday, Hong Kong leader Carrie Lam announced. She wore a face mask.
The virus has spread across China and to at least 16 countries globally.
On Monday, Germany and Japan confirmed that they had cases involving people who had not travelled to China but caught the virus from someone who had.
This had previously been seen only in Vietnam, which borders China and where someone was infected by his father who had travelled from Wuhan, the epicentre of the outbreak.
What’s Hong Kong’s plan?
Carrie Lam announced Hong Kong’s new strategy to tackle the virus on Tuesday.
In addition to suspending train and ferry services, flights to mainland China will be halved. People will also no longer be able to receive permits to visit Hong Kong from the mainland.
The city of seven million – a major financial centre – is part of China but retains significant autonomy.