"The German Federation of Journalists recommends journalists to avoid until further notice the use of search engines and e-mail services from Google and Yahoo for their research and digital communication," the union said in a statement.
It cited "scandalous" reports of interception of both companies' web traffic by the U.S. National Security Agency (NSA) and Britain's GCHQ.
"The searches made by journalists are just as confidential as the contact details of their sources and the contents of their communication with them," said Michael Konken, head of the union which represents about 38,000 journalists. He said there were safe alternatives for both searches and email.
The Washington Post reported on Wednesday that the NSA had tapped directly into communications links used by Google and Yahoo to move large amounts of email and other user information between overseas data centres. It said the programme was operated jointly with GCHQ.
Google's chief legal officer said it was 'outraged' at the apparent interception of data from its private fibre networks. The company declined to comment on the German union move. Yahoo said it had strict security in place at its data centres and had not given access to the NSA or other agencies.
Revelations by fugitive U.S. intelligence contractor Edward Snowden about the scale of NSA surveillance worldwide, from the alleged mass trawling of emails to the tapping of world leaders' phones, have caused international outrage.
The German government said last week it had evidence that Chancellor Angela Merkel's mobile phone had been monitored by U.S. intelligence.
Government snooping is especially sensitive in Germany, which has among the strictest privacy laws in the world, since it dredges up memories of eavesdropping by the Stasi secret police in former communist East Germany.
Earlier this month, Deutsche Telekom said it wanted German companies to cooperate to shield local internet traffic from foreign intelligence services, although experts believe this could be an uphill battle.
In August, Deutsche Telekom and its partner United Internet launched an initiative dubbed "E-mail made in Germany" to protect clients' email traffic.
© Thomson Reuters 2013