Bild newspaper reported officers with sniffer dogs scoured the flat while the politician was at home.
Hartmann has since cancelled all his upcoming professional appointments.
German news wire DPA and Bild both cited sources on Thursday which said Hartmann, the party’s interior policy expert, was suspected of buying crystal meth.
Germany’s interior ministry has been waging a campaign against the drug which has become more popular in the country over the last few years.
According to Bild newspaper, he allegedly caught the attention of police while buying drugs. The newspaper claimed Hartmann allegedly bought 100 grams of crystal meth, apparently for his own use.
The 51-year-old resigned as the SPD’s parliamentary spokesman for interior affairs on Wednesday but remains an MP.
The politician has been a member of parliament since 2002 and also sits on the parliamentary committee which oversees the security services, a position which he is also set to step down from, Süddeutsche Zeitung reported.
In December 2012 he spoke out against the legalization of 'soft drugs' including cannabis. "Cannabis is not a harmless drug," Hartmann said in response to a question from a voter.
Christine Lambrecht, leader of the centre-left SPD in parliament, said: “The SPD parliamentary fraction is supporting the work of prosecutors. The allegations must be cleared up quickly and fully.”
The district branch of Hartmann’s party in Rhineland-Palatinate said they were shocked by the allegations. “We’ve known Michael Hartmann for many years as a committed politician,” they said in a statement.
Prosecutors put in a request to lift Hartmann’s immunity on Monday so that his apartment could be searched. A court order giving them permission to do so was granted on Tuesday.
Hartmann is the second high-ranking SPD politician to step down in the past year.
Former chair of the parliamentary committee on internal affairs, Sebastian Edathy, quit in February "for health reasons." Later it emerged he was being investigated over allegations he had downloaded inappropriate photos of children.
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