But she praised the current Greek government for covering "much of the ground" required for recovery.
"I hope and wish that Greece remains a member of the eurozone," Merkel said. "As partners, we are working hard to achieve that."
Her visit triggered protests attended by some 50,000 demonstrators in Athens. The rallies were mostly peaceful, but police briefly clashed with several dozen demonstrators and detained nearly 200 people throughout the day.
Germany, Europe's largest contributor to the bailout fund that has rescued Greece from bankruptcy, is viewed by many Greeks as the primary enforcer of the austerity measures the Greek government enacted in exchange for emergency aid.
Debt monitors from the European Union, International Monetary Fund and European Central Bank, known as the "troika," will deliver a report in the coming weeks on whether Greece should receive its next bailout payment, without which it will likely go bankrupt.
Merkel, who stopped in Athens for five hours, said the coalition government led by Prime Minister Antonis Samaras still had to push through more key cost-cutting reforms.
"Much of the ground has been covered . . . There is daily progress," Merkel said after talks with Samaras. "This is an effort that should be seen through because otherwise it would make the circumstances even more dramatic later on."
Although the German leader dampened expectations in Athens of a stronger message of public support for Greece, Samaras said Merkel's visit had ended "the country's international isolation."
Greece has depended on bailouts from Europe and the International Monetary Fund since May 2010. To get the loans, it has implemented a series of deep budget cuts and tax hikes, while increasing retirement ages and facilitating private sector layoffs.
To date, Greece has received 240 billion euro ($310 billion) in bailout loans and has renegotiated a 110 billion euro ($142 billion) deal on the repayment of some of its bonds. However, Athens must pass further austerity measures worth 13.5 billion euro ($17 billion) over the next two years to qualify for its next rescue loan payment -- without which the government will run out of cash next month.