US civil liberties group the Electronic Privacy Information Centre (Epic) claims the app collects “massive amounts of personal information from users, including location data”.
Samsung says the complaint is baseless and it takes privacy seriously.
Jay-Z and Samsung teamed up to offer one million people the album for free.
According to Epic, the “Magna Carta app also includes hidden spam techniques” that makes users promote Magna Carta Holy Grail to their friends.
They say it also pulls in data from other accounts and other apps on the user’s phone.
The privacy group has asked the Federal Trade Commission (FTC), which protects consumers in the US, to suspend distribution of the app.
In a statement, Samsung said: “We are aware of the complaint filed with the FTC and believe it is baseless. Samsung takes customer privacy and the protection of personal information very seriously.
“Any information obtained through the application download process was purely for customer verification purposes, app functionality purposes and for marketing communications, but only if the customer requests to receive those marketing communications.
“Our permissions are in line with other apps’ standard permissions. Samsung is in no way inappropriately using or selling any information obtained from users through the download process.”
Previously Epic has complained about Snapchat, the publisher of a mobile app that deletes pictures and videos after they have been viewed, for “falsely” claiming they could be removed “forever”.
The Magna Carta Holy Grail app was released on 4 July with Samsung paying £3.2m for digital copies for its customers.
Cloned versions of the app were created by hackers. Available via unofficial sites, they contained code that unlocked anti-Obama messages.
Magna Carta Holy Grail is topping the Official Album Chart giving Jay-Z his first UK number one album.
Jay-Z has also announced details of his next European tour to support the album, with dates in Manchester, Birmingham and London.
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