Up to 50,000 businesses which provide alcohol, hot food or entertainment after 11pm may have to shut temporarily after failing to reapply for licences.
Most businesses that failed to apply were licences and takeaways
New licences will be needed from 24 November under the Licensing Act 2003.
Businesses had until midnight to apply for automatic extensions to their existing licences, and those which did not could now face delays getting them.
Many small businesses may face a "gap in trading", the Department of Culture, Media and Sport said.
It said the new law has been introduced to modernise the UK's licensing laws and reduce bureaucracy.
A spokeswoman said up to a quarter of the 190,000 businesses that needed to reapply failed to do so.
"They can still apply, but they could face a gap in trading," she said.
'Blood, sweat and tears'
However, businesses which missed the deadline will be forced to begin a fresh application, rather than converting their existing licence.
The new system will allow businesses to extend licensing hours and potentially sell alcohol all day.
Most pubs were believed to have applied already, but many small and late night restaurants are thought to have failed to do so.
Mark Hastings, as spokesman for the British Beer and Pub Association, described the process as being one of "blood, sweat and tears", adding that it had cost the pub trade £120m.
Mr Hastings also called for the licensing process to be simplified.
These sentiments were echoed by other business groups.
A spokesman for the British Hospitality Association criticised the procedure, saying: "It's very complicated and it's far more expensive than the old system".
He said "the smaller end of the market", such as "ethnic restaurants and kebab shops" had endured the most difficulties with the licensing system.
And a British Retail Consortium spokeswoman said: "It's been quite a burdensome process, often requiring lawyers to come on board to complete the process."