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The warning comes after the first such app - Natural Cycles - was given an official approval as a method of contraception.
In 2015
a clinical study
showed that the app was as effective as the pill.
The app works by getting women to enter their body temperatures, ovulation test results and date of menstruation.
An algorithm (a set of rules to help solve a problem, run by computer software) then determines whether a woman is fertile on that day.
This should help her make a decision about having unprotected sex.
But while sexual experts agreed fertility awareness apps have great potential to broaden contraception choice - three organisations warned on Thursday that being classed as a medical device doesn't guarantee the app will effectively prevent pregnancy.
Image captionThe app is used by more than 150,000 women in 161 countries.
The sexual health charity FPA, the Faculty of Sexual and Reproductive Health of the Royal College of Obstetricians and Gynaecologists (FSRH) and Dr Cecilia Pyper of the University of Oxford and FertilityUK said that these kind of apps often have complicated instructions that need to be strictly followed, if they are to be effective.
Natural Cycles was approved as a class IIb medical device by Tüv Süd, which means it can now be marketed as a hormone-free, non-invasive contraceptive option.
Image captionFertility awareness apps are based on fertility awareness methods - also known as natural family planning
Dr Elina Berglund, co-founder of Natural Cycles, said: "Women around the world are interested in exploring effective non-hormonal, non-invasive forms of contraception - and now they have a new, clinically verified and regulatory approved option to choose from.
"Our high quality clinical studies, together with the required regulatory approvals, means we can provide women everywhere with a new option for contraception."
Image captionWomen enter their temperature into the app to try and determine their fertility
But is natural contraception the best way in preventing unwanted pregnancy?
"It's important when considering contraception that women aren't misled into thinking that non-hormonal contraception, whether that's the IUD, condoms or fertility awareness, is always a better choice than hormonal contraception," says Natika Halil, from the Family Planning Association.
"Although hormonal contraception has some potential side-effects and health risks, it can also have a range of benefits such as controlling menstrual bleeding, reducing PMS symptoms and managing acne."
Image captionNatural Cycles is said to be as effective as the pill
Dr Cecilia Pyper from Fertility UK said more research needs to be done into fertility apps.
"There are currently hundreds of fertility apps and period trackers and no system to evaluate these technologies, which are changing at a very fast pace.
"The research we do have suggests that many are ineffective at accurately predicting a woman's fertile days.
"Large, independently-conducted prospective trials are needed before apps can be considered for contraceptive use."
(BBC)
