From May 20 onwards Ryanair will charge customers £5 to check in online.
Currently the only way to avoid additional costs and purchase a cheap ticket is to use the online check-in service, take hand luggage only and pay via Visa Electron.
Any customer who has paid the £5 charge but has been unable to print the boarding pass will be charged £40.
Ryanair is also pushing ahead with plans to deter passengers from checking in luggage.
Currently it charges a £5 fee per item of hold luggage in advance however this is set to double from May 20, with additional bags charged at £20 each.
Hidden extra costs of budget airlines such as Ryanair have been criticised by consumer groups and the media alike. Ryanair's other additional charges include £5 for paying by debit card (other than Visa Electron) while in February it announced it would look at putting a £1 coin slot in the doors of its toilets.
Ryanair's move comes as it and other European budget airlines come under pressure from EU authorities to reform what it believes are misleading websites.
Among the EU's concerns are the lack of clarity about tax and additional costs and the use of pre-ticked boxes which force consumers to opt out of extra charges like insurance.
An EU review of around 70 airlines' booking sites in March found that only 16 of them conformed to its regulations.
Officials are expected to announce today that around 50 airlines, including Ryanair and EasyJet, are set to improve their sites or have done so already.
The EU is not the only one to have issues with the Ryanair site. In February blogger and web developer when he revealed a flaw in the site which allowed people to book flights for a charge of £0.00.
Later that day Rowe received the following reply: "Jason! You're an idiot and a liar!! fact is! You've opened one session then another and requested a page meant for a different session, you are so stupid you don't even know how you did it! You dont get a free flight, there is no dynamic data to render which is prob why you got 0.00.
"What self respecting developer uses a crappy CMS such as word press anyway AND puts they're mobile ph number online, I suppose even a prank call is better than nothing on a lonely sat evening!!"
The respondent's IP address was tracked to Ryanair's offices, whereupon the airline confirmed a member of its staff was behind the message.
It did not apologise for the abuse but said it would in future ban its employees from communicating with "lunatic bloggers".