The fishingrodlicence.com website adds a £14 charge for "checking" applications.
The Angling Trust said the service was of no benefit to anglers because the Environment Agency (EA) does not require applications to be checked before submission.
As well as the extra charge, anglers buying their licences from the web site will not be able to go fishing until they receive their licence in the post.
The EA site offers a receipt and reference number which does allow people to fish while they are waiting for the licence to arrive.
The Angling Trust strongly recommends that all freshwater anglers buy their licence direct from the Environment Agency over the phone or via its website here, or from Post Offices and clearly authorised outlets.
The AT is raising the matter with Fisheries Minister Richard Benyon MP and Charles Walker, Chair of the All Party Parliamentary Angling Group.
Mark Lloyd, Chief Executive of the Angling Trust said: "This site offers no real extra service, but demands a 50pc surcharge on top of the rod licence fee and we urge all anglers to spread the word.
"We would encourage members who have concerns about this website to contact Consumer Direct and their MP.
"Any unsuspecting new anglers trying to buy their first licence might be put off by the inflated price and decide not to take up fishing."