Heiko Maas said he no longer had confidence in Harald Range, dismissing his statements as “incomprehensible”.
Prosecutors are investigating whether the Netzpolitik website revealed state secrets in articles about plans to step up state surveillance.
News of the case sparked street protests last week over press freedom.
The outcry put the German government on the back foot, with senior officials stressing that Germany was committed to press freedom and casting doubts over whether the articles constituted treason.
On August 4, in a rare public row between the German judiciary and the state, Harald Range said the government had asked him to drop an independent investigator from the inquiry, who concluded that one of the articles published did amount to a disclosure of a state secret.
The request, said Harald Range, amounted to “an intolerable encroachment on the independence of the judiciary”.
He said that while the freedom of press was valuable it was not “limitless”.
Minister Heiko Maas responded at a news conference in which he called Harald Range’s comments “incomprehensible and misleading”.
He said his trust in the prosecutor’s ability had “suffered lasting damage” and he had requested his dismissal.
Harald Range, who is 67-year-old, was due to retire in 2016. Munich’s chief public prosecutor, Peter Frank, has been named by Heiko Maas as his successor.
The state investigation, into two journalists at Netzpolitik.org, is currently paused. The journalists have called for the case to be dropped.
Their first story, in February, alleged that Germany’s domestic intelligence agency wanted additional funds to increase its online surveillance program.
A later article in April concerned the spy agency’s efforts to set up a special unit to monitor social networking websites.
Critics have accused Harald Range of double standards, with the prosecutor earlier this year dropping an investigation into alleged tapping of Chancellor Angela Merkel’s phone by the US National Security Agency (NSA) over lack of evidence.
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