The Defence Ministry announced that Guttenberg set off late on Wednesday for his ninth trip to the country, where he will meet with troops serving as part of the NATO mission there.
But unlike previous visits to Afghanistan, this time Guttenberg was unaccompanied by journalists. Further details were set to be released later on Thursday.
Chancellor Angela Merkel accompanied Guttenberg on his last journey to Afghanistan just before Christmas 2010.
Since then, the conservative Bavarian Christian Social Union politician has come under fire for a number of scandals within the military. Among them are the death of a woman sailor on board the navy training ship Gorch Fock and the shooting of a soldier in Afghanistan, which may have occurred during a game involving guns.
On Wednesday, Guttenberg was accused of plagiarizing portions of his doctoral thesis at the University of Bayreuth. The minister said he had nothing to worry about, but on Thursday further accusations about other uncited sources surfaced.
News magazine Der Spiegel reported Guttenberg had filched four sentences about the history of the United States' constitution from the US embassy's website without citation. But later in the dissertation the embassy is cited in another context, according to the magazine.
Prof. Barbara Zehnpfennig called for Guttenberg's doctorate to be revoked after saying she was the original author of several passages in his thesis.
"It beats me how someone can be so blatant," Zehnpfennig told daily Die Welt.
Guttenberg - or Karl-Theodor Maria Nikolaus Johann Jakob Philipp Franz Joseph Sylvester Freiherr (Baron) von und zu Guttenberg, to give the aristocrat his full name - regularly tops surveys as Germany's most popular politician.
But he is also a popular target for the German press, and the latest episode could turn out to be the most damaging to his political career according to some observers.