Chief prosecutor Harald Range took the unusual step of openly accusing Justice Minister Heiko Maas of "an intolerable encroachment on the independence of the judiciary".
The case centres on the Netzpolitik.Org (Net politics) blog, which earlier this year published documents on plans by Germany's domestic security agency to expand its Internet surveillance.
Last Thursday the blog revealed that Range's office had launched a treason investigation into two of its writers -- Germany's first such probe against the media in over half a century.
On Twitter #Landesverrat (#treason) became a top trending topic and the case sparked a Berlin street rally and online petitions in support of Netzpolitik.
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The controversy has flared amid persistent anger over the US National Security Agency's mass surveillance activities revealed by fugitive intelligence contractor Edward Snowden, and questions about the extent of German cooperation.
But today the 67-year-old chief prosecutor shot back.
He said the independent expert had agreed that the documents appeared to be state secrets, as asserted by domestic security agency chief Hans-Georg Maassen.
Range said he had informed the justice minister of this but was told "to immediately stop" the process of commissioning outside advice.
The chief prosecutor said he had complied, but he added angrily that "to exert influence on an investigation because its possible outcome may not be politically opportune represents an intolerable encroachment on the independence of the judiciary".