Merkel's comments at the Munich Security Conference, an annual gathering of top global defense and foreign policy officials, followed days of tension between Washington and Europe over Iran.
Merkel said the split over Iran "depresses me very much," but she downplayed the substance of the differences.
"I see the ballistic missile program, I see Iran in Yemen and above all I see Iran in Syria," she added.
But "the only question that stands between us on this issue is, do we help our common cause, our common aim of containing the damaging or difficult development of Iran, by withdrawing from the one remaining agreement? Or do we help it more by keeping the small anchor we have in order maybe to exert pressure in other areas?"
Merkel also questioned whether it's good for the U.S. to withdraw troops quickly from Syria "or is that not also strengthening the possibilities for Iran and Russia to exert influence there?"
Turning to nuclear disarmament, Merkel said that the U.S. announcement earlier this month that it was pulling out of the 1987 Intermediate-Range Nuclear Forces treaty was "inevitable" because of Russian violations.
Moscow followed suit, strongly denying any breaches. The U.S. administration also has worried that the pact was an obstacle to efforts to counter intermediate-range missiles deployed by China, which is not covered by the treaty.
Merkel noted that the end of a treaty conceived "essentially for Europe," where such missiles were stationed during the Cold War, leaves Europe trying to secure future disarmament to protect its own interests.
She said that "the answer cannot lie in blind rearmament."
"Disarmament is something that concerns us all, and we would of course be glad if such negotiations were conducted not just between the United States ... and Russia, but also with China," she said.
Merkel also defended Germany's progress in fulfilling NATO guidelines for countries to move toward spending 2 percent of gross domestic product on defense, which have been criticized as too slow. And overall, she rejected the idea of go-it-alone foreign policy.
"Now that we see great pressure on the classic order we are used to, the question now is: do we fall apart into pieces of a puzzle and think everyone can solve the question best for himself alone?" she said, adding that it's better to "put yourself in the other's shoes ... and see whether we can get win-win solutions together."
Moulson reported from Berlin.