Prosecutor Harald Range last week suspended the investigation into netzpolitik.org while he awaited an independent expert opinion on whether the website had revealed state secrets by publishing plans to step up state surveillance of online communications.
Privacy is an especially sensitive issue in Germany after the extensive surveillance by Communist East Germany's Stasi secret police and by the Gestapo in the Nazi era.
Justice Minister Heiko Maas said last week that it was important to defend the independence of the press, adding he doubted whether the publication of the documents would endanger Germany.
In a rare clash between the state and judiciary, Maas said on Tuesday he no longer trusted Range after his accusations of political interference and his decision to go public.
"The remarks and the chosen course of action by the federal prosecutor today are not comprehensible and give the public a false impression," the minister told a news conference in Berlin.
"Therefore I decided in agreement with the chancellery that I will ask the president to retire (the prosecutor)," Maas said, adding that he would name Munich's chief public prosecutor, Peter Frank, as successor.
A spokesman for the prosecutor's office declined to comment.
Earlier on Tuesday, Range told journalists in the southwestern town of Karlsruhe: "Influencing investigations because the result they might have doesn't seem politically opportune is an intolerable intervention in the independence of the judiciary."
Maas said both sides had agreed on Friday that the justice ministry would assess whether the publication amounted to revealing state secrets and that Range's idea of an independent expert opinion should be dropped.
The minister noted that at this point Range had not told him yet that the judicial expert was leaning toward the opinion that the publication of the internal documents was a case of treason.
Netzpolitik acknowledged in its reports that excerpts it had cited were either intended to be dealt with by a closed parliamentary committee or were from a restricted official document.
A spokeswoman for Angela Merkel said on Monday that the justice minister had the chancellor's full support. The interior ministry also said it had doubts about the accusation of treason.
(Additional reporting by Norbert Demuth in Karlsruhe and Michelle Martin in Berlin; Editing by Ruth Pitchford)
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