About 2,000 people are understood to have downloaded the fake app from the Android online market while hundreds more tried it on their iPhones.
It is thought that customers had not yet been asked to part with any cash. However, many applications only charge customers after 30 days of use.
A spokeswoman for RTE confirmed the software was no longer available from the Apple application store.
"This app is in no way affiliated with or approved by RTE or Vision Independent Productions -- the producers of Operation Transformation," the spokeswoman said.
"Operation Transformation is a free public service and participation does not depend on spending money on what is an illegal piece of software."
An advertisement for a mobile phone company, which appeared on the application's online page, suggested that it was created in the UK.
"All Operation Transformation videos, recipes, exercise routines and materials are available free of charge at www.rte.ie/ot and www.myot.ie," an RTE representative added.
Myot.ie is a mobile-enabled website that allows viewers to register their measurements and create their own weight-loss plan, based on the show.
While online users were disappointed to have been conned by the app, many remarked on the series' Facebook page that they would love for TV producers to launch an official Operation Transformation phone application.
And it appears that the team behind the popular RTE series appears to be considering it for next season, according to the message they posted to fans.
"We did not have the resources to develop a fully featured app which would work across all mobile platforms and it has always been important to us that the information should be freely available to all those who wish to access it.
"We will absolutely look at developing apps for next season," an online representative for Operation Transformation assured fans.
"In the meantime, many thanks to the more than 53,000 people who registered to use myot.ie.
"Log in issues aside, we hope you found it useful!"
The fifth season of Operation Transformation has attracted a huge community of online followers.
The series website has had over 4m hits and 2.4m visitors so far.
Nearly 600,000 viewers also tuned in for the first episode of the diet and exercise programme.
A TV insider said:"There's a whole Operation Transformation community out there supporting one another and organising their own fitness challenges -- which is the way it should be for successful weight loss."