Agriculture Minister Hans-Peter Friedrich, who was then interior minister, has come under fire for tipping off the party chief of a prominent MP that the lawmaker was under investigation.
"I offered Chancellor Angela Merkel my resignation today from my post as federal agriculture minister," Friedrich said in a hastily called televised statement.
He reiterated earlier remarks that he believed he had "acted politically and legally correctly".
"But I will also say that the pressure on me has grown so much in the last few hours that the duties...In the agriculture ministry can no longer be handled with the necessary concentration, calm and political support," he said.
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The case has blown up after news broke early in the week that searches had been carried out at the home and offices of Social Democrat (SPD) lawmaker Sebastian Edathy as part of a child pornography investigation.
Edathy -- who has gained prominence for heading a parliamentary panel into the shock 2011 discovery of a neo-Nazi killer cell -- had stepped down from his Bundestag seat days earlier citing health reasons.
He has vehemently denied in an Internet-posted statement being in possession of child pornography.