The move is an attempt by Beijing to ease growing anger in Hong Kong over shopping trips by mainlanders who are take advantage of lower taxes.
Shenzhen residents will now only be able to enter Hong Kong once per week, and stay for no longer than a week.
Hong Kong officials say 47 million visits were made in 2014 by mainland Chinese people.
About a tenth of those visits were by people who entered Hong Kong more than once a week, a large proportion of them Shenzhen residents holding multiple entry visas.
Many of the visitors buy up household goods in bulk to resell across the border – as Hong Kong does not charge sales tax – despite this being illegal.
There have been angry protests in recent months over this so-called parallel trading, occasionally resulting in scuffles in shopping malls close to the border.
China’s Xinhua news agency, citing the ministry of security, said on April 13 that the new rules applied immediately.
It said the decision had been made because of concerns that Hong Kong was struggling to cope with the huge numbers of tourists.
Hong Kong’s Chief Executive CY Leung welcomed the move, saying he had raised the issue with Beijing in June.
Mainlanders have to get permission from their government to enter Hong Kong.
CY Leung warned that existing visas would remain valid, meaning it could take some time for the effect of the change to be seen.
He also cautioned that the “unruly protests” seen in towns close to the border had actually hampered the discussions and “hurt the feelings between the people of Hong Kong and the mainland”, the South China Morning Post reports.
Parallel trading has been a key factor in the growing anti-mainland sentiment in Hong Kong.
There is huge demand in China for household items from Hong Kong, in particular milk powder, as they are seen as being both cheaper and better quality.
Hong Kongers say this trade pushes up costs and causes huge delays at border crossings, while also complaining about poor behavior from mainlanders.
The authorities on both sides of the border routinely arrest people caught smuggling and crack down on commercial operators, but locals have long demanded more decisive action.
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