A German regulator on Tuesday slapped a three-month ban on Facebook collecting user data from WhatsApp accounts and referred the case to an EU watchdog, citing concerns about election integrity.

The Hamburg Commissioner for Data Protection and Freedom of Information, which has jurisdiction because Facebook's German branch is based in the city, sent the order to the social network which owns the popular messaging service.

The tech giant informed WhatsApp users earlier this year that they must consent to a new data use policy to continue using the service.

The German authority said in an emergency decision that the terms of that agreement were now null and void in Europe's top economy for three months.

It will hand the case over to the European Data Protection Board, an independent EU body that enforces rules throughout the 27-nation bloc.  

The head of the German regulator, Johannes Caspar, said past Facebook data protection breaches as well as Germany's general election in September showed the "dangers" of "mass building of user profiles" that could be exploited.

"This ruling is intended to protect the rights and freedoms of the many millions of user across Germany who give their permission to the new use and privacy policy," he said.

"That includes not only the private sphere but also the possibility of using profiles to influence voter choices and manipulate democratic decisions." 

Caspar noted that with nearly 60 million users in Germany WhatsApp was "by far" the country's most popular social media app. 

WhatsApp on Friday stepped back from its plan to require users to accept the new terms which critics said could expand data collection from its two billion users around the world.

The service, which was set to enforce its new data-sharing policy on May 15 -- following a delay in response to a user outcry -- said on its website that it would not immediately cut off users who don't accept the new terms, although it would send reminders to those who don't opt in.

The update will allow additional sharing of information from WhatsApp with Facebook and its other applications such as Instagram and Messenger, such as contacts and profile data, but not the content of messages which remain encrypted.

A WhatsApp spokesman said the German order "is based on a fundamental misunderstanding of the purpose and effect of WhatsApp's update and therefore has no legitimate basis".

He said the update actually "provides further transparency about how we collect and use data".

As the Hamburg authority's "claims are wrong, the order will not impact the continued roll-out of the update," he added.