The low cloud conditions prevented Merkel from travelling via helicopter between German military bases in the northern city of Mazar-i-Sharif and Faisabad, so she is now on her way back to Berlin with plans to land midday.
Merkel arrived in Afghanistan on Monday to visit Bundeswehr troops in Kunduz just after alliance leaders pledged thousands more troops to operations in the troubled country at NATO's 60th anniversary summit.
The mission, Germany's first major overseas military operation since World War II, has always been highly unpopular. Thirty-one German troops have died in Afghanistan since 2002, including 14 during attacks.
The German contingent, which parliament voted last year to increase to 4,500, is part of the NATO-led International Security Assistance Force (ISAF). The soldiers are based in the relatively peaceful north of Afghanistan, though they have come under attack more frequently in recent months.
Merkel said during her visit that keeping a high presence of German troops in the country would help Afghanistan to eventually address its own security concerns.