Fifty-nine people have been issued with year-long bans that prevent them  from entering most licensed city venues, compared with 20 long-term bans issued in Kings Cross, NSW government data shows.

One venue, Hotel Chambers in Martin Place, is being prosecuted for two breaches of the  city  lockout laws.

The alcohol-violence laws also impose annual fees on venues serving alcohol from next March. Extra loadings will be charged for late trading hours and the scheme will be expanded in 2016 to charge more for larger venues, risky locations and a track record of violent incidents.

But the introduction of risk-based licensing is  likely to be more difficult than politicians had anticipated.

The NSW government was in the dark over how many restaurants, clubs, bottle shops, theatres, karaoke bars, tourism and sports venues actually served alcohol in NSW, after more than a quarter of liquor licence holders failed to lodge returns on time this year.

The maximum penalty for failing to provide updated information to the regulator every two years on trading hours, venue size, staff numbers and ownership is 12 months' prison.

Despite this,  4757 out of 18,591 venues failed to meet a March deadline, and last month more than 3000 were still outstanding. The Office of Liquor, Gaming and Racing said it was investigating 550 venues and had fined 15, but believed some venues were no longer trading.

The government had predicted it would collect $20 million in fees under the new licence system, meaning it would cover its costs.

But the high proportion of "ghost" licences is likely to result in a revenue shortfall, or increased enforcement costs.

From next year, liquor licences will be cancelled if venues fail to pay the new fee within 56 days.

Invoices will be issued to all venues in April, regardless of whether or not they lodged a return this year.

"NSW has been slow out of the blocks in implementing modern liquor licensing, which is precisely why the NSW  government is introducing periodic licensing and increasing the opportunity for the regulator to have appropriate regular contact with licence holders," said a spokeswoman for the Hospitality, Gaming and Racing Minister,  Troy Grant.

The NSW director of liquor and policing for the Australian Hotels Association, John Green,  said 93 per cent of the 2200 hotel licensees had completed their returns.

"Of the small number of hotels which haven't lodged returns in the 2013-14 period, many are non-members, the premises are closed or the licence is dormant," he  said.

Half of all liquor licences were on-premises licences, typically used by restaurants, cafes, theatres and sports venues. The next biggest category was bottle shops.

The Australian Liquor Stores Association and Woolworths had complained to the Abbott government's Competition Policy Review that the risk-based licensing scheme was "inequitable".