"I have commissioned the chief of staff to conduct a review of all branches of the military to see the extent to which there were in recent years and still are indications of practices that contradict the Bundeswehr's principles," Guttenberg told daily Bild am Sonntag.
The defence minister said the review would also help clarify what consequences should result for misconduct.
Guttenberg's remarks come as the defence ministry faces ongoing questions about both an alleged "mutiny" on board a German navy training vessel, as well as the circumstances surrounding the death of a soldier in Afghanistan.
Critics claim the defense ministry failed to provide adequate information to the German parliament and even misinformed members of the Bundestag on the latter incident – a charge that Guttenberg has rejected.
Responding to calls by the Social Democrats' parliamentary group leader, Frank-Walter Steinmeier, to admit his mistakes, Guttenberg said there is "no reason" to do so.
Bild am Sonntag reported that a delegation of 15 Bundestag lawmakers, including members of the SPD, Christian Democrats, Free Democrats and Greens, traveled to Mazar-i-Sharif in Afghanistan just days after the soldier's death.
The parliamentarians were reportedly given the chance to speak to soldiers with detailed knowledge of the incident and were told that the victim was accidentally hit with a bullet from a comrade's weapon.
Last week, a report to the parliamentary armed services committee said the soldier was shot following an apparent weapons game at an outpost near the German base of Kunduz in late 2010.
In comments made to Bild am Sonntag, Guttenberg said the military review would also examine whether careless handling of weapons was an issue.
Meanwhile, the defence ministry has also come under fire for its handling of reported misconduct on board the Gorch Fock navy training ship.
Four crew members were allegedly accused of "mutiny" when the crew refused to climb the rigging of the historic ship, after one of their comrades, 25-year-old Sarah S., fell 27 metres to her death last November.
Guttenberg announced Saturday he had fired the Gorch Fock's commander, Captain Norbert Schatz – sparking criticism from members of the political opposition.
Left Party leader Klaus Ernst said the defence minister needed to conduct a full investigation, not find a "sacrificial pawn."
"If we don't get all the facts on the table immediately, then the Bundestag will have to seriously consider whether the incidents in the Bundeswehr don't warrant a more in-depth investigation," Ernst said on Saturday.
The mother of the sailor who died on board the Gorck Foch has reportedly brought charges against the German government, saying she believes the true cause of her daughter's death has been "covered up."
"No one has told me what exactly happened when my daughter died," she told magazine Focus.