"We will not gloss over anything, but we will not accept any premature condemnation," she said.
"I refuse to tolerate that, either from Germany or from abroad."
Earlier on Tuesday, the Nato-led force in Afghanistan said it believed civilians were killed or injured in Friday's strike, after previously saying that civilians were only harmed.
General Stanley McChrystal, the head of international forces in the country, has ordered an investigation into the bombing.
The strike was reportedly ordered by a German commander after Taliban fighters hijacked two fuel trucks on a Nato supply route from Tajikstan.
Hamid Karzai, the Afghan president, called the decision a major "error of judgment".
Bernard Kouchner, the French foreign minister, also called the airstrike a "big mistake", while Javier Solana, the EU foreign policy chief, said it was a "very, very sad event".
But Merkel defended Germany's role in Afghanistan, where it has more than 4,200 troops stationed.
"No one should deceive himself: the consequences of not acting will be attributed to us just as much as the consequences of acting," she said.
"Everyone who calls for Germany to step aside from fighting international terrorism, particularly in Afghanistan, should consider that."
The chancellor said she had spoken to Gordon Brown, the British prime minister, and Nicolas Sarkozy, the French president, about beginning a new era in the country.
"Now is the right moment, together with the new Afghanistan leadership, to set out at the end of this year how this transfer of responsibility will happen," she said.