Licensees who failed to get their licensing applications in before the August 6 deadline could find themselves facing closure if there are objections.
Many local authorities are privately admitting that the volume of objections received means they are unlikely to get hearings completed before the November 24 deadline.
Under the Licensing Act, pubs are only guaranteed to keep their existing licences if they applied before the August 6 deadline. Those who applied after that and have been subject to objections from residents could now find themselves forced to close at the start of the new regime, until their council can stage a hearing.
The situation could cause further problems for scores of licensees who have been forced to apply from scratch after being let down by their legal advisers, consultants or agents.
Lesley Cameron, head of licensing at St Albans City & District Council, confirmed the council would be "unable to meet the timescales" because of a backlog of applications. She said: "Our residents are aware of their rights and the law and a lot of applications are being contested. It's mainly residents and a lot of our pubs are in residential areas."
Jackie Kennedy, head of licensing at Birmingham City Council, claimed the council was "well on top" of current applications.
"The only danger is where pubs and bars have not sent in their applications," she added. "But some of the smaller local authorities may have been swamped. There is always the danger of an independent pub missing out."
However, Rachael Rogers, policy officer at LACORS, the local authority co-ordinating body, said: "Local authorities have been bending over backwards. If people have missed the August 6 deadline for grandfather rights they need to get their applications in.
"A local authority is bound under statute to have a licensing hearing if there are objections."
Pictured: Hackney Council in London has launched an innovative postcard campaign to encourage the last remaining licensed premises to get their new applications in.