Fans of Beyonce and One Direction have been affected
Viagogo, Seatwave, Getmein and Stubhub claim buyers always get a valid ticket.
But an investigation by Radio 4's You and Yours found a vendor was able to make a fortune selling fake e-tickets to unsuspecting fans.
The firms said they took fraud very seriously and that customers who don't get valid tickets were refunded.
Secondary ticketing websites act as marketplaces, allowing sellers to charge what they like for popular gigs, with the site earning a commission on top.
The sites tell the public they can guarantee valid tickets by only paying sellers after the buyer has attended the concert.
Despite that promise, some sellers can be paid before the event - if they achieve trusted status with established periods of successful ticket sales.
The programme learned one tout established himself as a trusted seller last year, only to suddenly issue thousands of printed, fake duplicates of e-tickets - resulting in a big increase in excited fans arriving at venues to find someone is in their seat, and that their ticket is worthless.
Kings of Leon fan Clifford Richards, 21, from Cornwall, thought he was about to see the band at the O2 in London.
He said: "I bought tickets from Getmein. We went in, got through the barriers, she scanned the barcode and looked at me a bit funny and called a supervisor over.
"They said the tickets were duplicates and we wouldn't be allowed in."
Reg Walker is a ticketing expert at The Iridium Consultancy which advises venues across the UK on fraud prevention.
He said he had seen a massive surge in counterfeit and invalid tickets sold through the four sites this year, adding: "In the last four months alone we've seen over 2,000 of them."
"We've seen more counterfeits in one venue than we've seen in the preceding six years. In the majority of cases the barcode is for another event or it's the same barcode from one ticket resold over and over again."
Senior Trading Standards officer James Williams described the guarantees offered by the companies as "not worth the paper they were written on".
Stuart Cain, head of ticketing at Birmingham's LG Arena, said: "On a big show where there are a lot of e-tickets you can get up to 100 people a night affected.
"It's supply and demand, the e-touts know which concerts to go for."
When asked what action was being taken, the four sites told the programme that, if they discovered suspicious activity on their sites they would cancel tickets and replace them. Or if they were unable to provide replacements, the customer would be refunded.
