Hans-Peter Friedrich was forced to quit from the agriculture portfolio Friday under pressure over suspicions he leaked confidential information about the probe while serving as interior minister.
Replacing him is Christian Social Union (CSU) party colleague Christian Schmidt, who is currently the party's deputy head, the Bavarian-based conservative party announced today.
The scandal built up steam last week as it emerged that Friedrich had tipped off the head of the Social Democratic Party (SPD) that the name of one of its prominent MPs had cropped up in an international child pornography inquiry.
German media has raised fears that the leak may have harmed the course of the legal investigation.
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The crisis has exposed traditional fault lines between Merkel's conservative bloc and its old foes, the centre-left SPD, who in December buried the hatchet to team up in a left-right "grand coalition".
It has also triggered awkward questions over who knew what and when as well as finger-pointing, just as the government grapples with political hot potatoes such as renewable energy and the minimum wage.
"For the chancellor it is important that all outstanding questions are settled in a convincing way," Steffen Seibert said.