Fewer than one in 12 underground stations and one in five overland stations in London have secure status, figures show.
All London stations are to be fitted with the latest CCTV technology
The government's Secure Stations scheme assesses management, CCTV and design.
Transport for London (TfL) said it was confident all stations met the criteria but they had simply not applied for the relevant certificate.
Of the 257 Tube stations only 20 have a certificate and 66 of the 358 overland stations have one.
A further 30 have lapsed since the scheme's 1998 launch including Waterloo, Westminster, London Bridge, Oxford Circus and Charing Cross.
A TfL spokesman said there are 6,000 CCTV cameras on the network and 700 British Transport Police on patrol.
"London Underground is confident that all of its stations meet and exceed the criteria of the Secure Stations scheme," he said.
"The scheme doesn't really deliver anything for the underground except a certificate to state that it has been accredited."
He added that TfL London Rail is two years into a five year investment strategy which will mean every suburban train and all 304 London wide stations being fitted with the latest CCTV technology.
A spokeswoman for the London Transport Users' Committee said the scheme needs to be better recognised so that passengers could feel assured CCTV is working and lighting is safe.
"We would encourage all train operators, Transport for London and the government to get together to make people feel safe," she said.
Liberal Democrat MP Paul Burstow said the figures given in Parliamentary answers will be of considerable concern to commuters in London, especially in the current climate.
He said: "With the recent terrorist attacks on our transport system and the London Olympics on the way, the need to tighten up security at London's stations has never been greater."