In her annual New Year address published on Monday, Merkel said: "In fact, the economic environment next year will not be easier, but more difficult," adding: "The crisis is a long way from being beaten."
Although top exporter Germany has managed to hold up to the crisis fairly well, growth has slowed here since the beginning of the year.
After expanding by 0.5 percent in the first quarter of 2012, gross domestic product (GDP) grew by just 0.3 percent in the second quarter and a mere 0.2 percent in the third quarter.
In October, the government slashed its forecast for economic output next year to 1.0 percent, compared to 1.6 percent previously seen.
The country's gloomy central bank has said Germany may even flirt briefly with recession early next year.
The Bundesbank also forecast that Germany would only grow by a meagre 0.4 percent in 2013.
Nevertheless, "it has been possible this year to have the lowest unemployment and the highest level of employment since reunification" in 1990, Merkel recalled.
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And a slowdown next year "should not leave us discouraged but should spur us on", said the chancellor, according to the text of her speech released in advance by her office.
Turning to the eurozone's efforts to tackle its three-year debt crisis, she judged that "the reforms that we have decided are beginning to work. However, we still need more patience. The crisis is a long way from being overcome."
Merkel also called for better supervision of the financial markets, stressing: "The world has still not sufficiently learned the lessons of the devastating financial crisis of 2008."