Returning from talks in Pakistan, Thomas De Maiziere was due to meet his Afghan counterpart Abdul Rahim Wardak, as well as President Hamid Karzai on the unannounced visit.
De Maiziere stressed Germany's commitment to the mission, two days after Merkel cast a shadow of doubt on Germany's planned withdrawal from Afghanistan in 2014, pointing to as yet unstable conditions for an exit of German troops.
In a news conference with Wardak, De Maiziere said: "I underlined that the German commitment, as agreed with the international community, is still valid and reliable."
"That means: together in, together out and that also means a confirmation of the timetable, with the mission finishing at the end of 2014," he added.
On Monday, during an unannounced visit to troops stationed in Mazar-i-Sharif in the north of Afghanistan, Merkel said the point had not yet been reached where Germany could say "we can pull out today."
"And therefore, I can also not say that we will manage that by 2013/2014. The will is there, we want to do that and we are working towards that," she said, according to German news agency DPA.
In later comments, she appeared to clarify her position, stressing: "2014 is the withdrawal date."
The minister's visit also came in the wake of Sunday's shooting spree by a US soldier who killed 16 Afghans, most of them women and children.
The tense atmosphere continued after suspected Taliban insurgents opened fire Tuesday on an Afghan government delegation attending a memorial service for the civilians who were murdered.
Karzai has described the massacre as "unforgivable" while Merkel said it was a "dreadful act."
Germany is the third biggest supplier of troops to the 130,000-strong NATO-led International Security Assistance Force (ISAF) after the United States and Britain.
It had 4,900 soldiers in Afghanistan as of February 1, but another 500 are set to be withdrawn by 2013 before a complete pullout.
Fifty-two German soldiers have been killed, 34 of them through enemy action, according to the military's website.
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