The Security Industry Authority (SIA) has been left struggling to cope after being swamped by applications last year.
A new law, which came into effect in November, means nightclub bouncers and private security workers must hold a licence.
One city nightspot was forced to draft in bouncers from Newcastle after some staff were left unable to work while waiting to be checked out. SIA bosses said they were on course to reduce the waiting list, which they say was caused by the volume of applications they received at the same time.
Today's fears were sparked by the case of Stuart Bavidge, a convicted sex offender caught working at a city Farmfoods store using a fake SIA letter.
Bavidge, 30, of Edinburgh, was given a three-year sentence for obtaining sexual favours by fraud after he forced his terrified 21-year-old victim to commit a sex act by pretending to be a policeman.
Although it is illegal to work without a licence, some security staff have remained in their posts while the SIA concludes its vetting. Anyone with a criminal conviction is refused a licence under the tough controls, and those flouting the laws can face up to five years in jail.
Police chiefs said that officers had checked out hundreds of door staff working in the city centre and found "very few" still waiting for their licences to be processed.
Inspector Bruce Johnston, sector inspector for the city centre, said he was aware of SIA "delays", but was confident every bouncer would be licensed within the coming months.
He said: "There are hundreds of door staff working at pubs and clubs and we want to see them all badged because it means they're trained in first aid and conflict resolution. In the past, many of the door staff were thugs, but now they do a highly professional job and can operate as our eyes and ears on the ground."
The licences ensure door and security staff are given background checks, undergo training and sit exams with a recognised firm. Companies supplying unlicensed workers face an unlimited fine and jail sentence of up to five years, while any establishment employing unlicensed door supervisors risks losing its premises' licence.
Bill McGregor, general manager of the Lava & Ignite club in Tollcross, said: "We have 12 door stewards and they are all licensed. A couple of months ago I had to bring up Luminar Leisure staff from Newcastle because of the SIA delays. We won't use staff who are unlicensed.
"This scheme does important work and making sure our staff are properly vetted and trained is good for our customers."
An SIA spokeswoman said: "Some licenses are taking nine to 12 weeks to process because the legislation only came in on November. Many people waited until then to send in an application so we received many at once. Each has to be thoroughly checked and that takes some time."