With six crucial state polls looming next year, Merkel is under the gun to get her centre-right alliance on track.
Merkel scraped to victory, with her conservative Christian Union bloc on September 27, 2009, allowing her to dump her unloved coalition partners, the Social Democrats (SPD), and link up with the pro-business Free Democrats (FDP).
But after 11 years of dreaming of reuniting in government, the two sides have been at constant loggerheads over core issues, allowing the SPD and the resurgent Greens to capture a clear ruling majority in opinion polls.
Merkel prefers to remain above the fray but analysts say she needs to reassert her authority if she hopes to see out her four-year term.
"She has got to lead, she has got to take some decisions, and she must force the smaller parties in her coalition to toe the line if she wants to survive," Manfred Güllner, head of the independent polling institute Forsa, told news agency AFP.
Bitter infighting over tax breaks, healthcare reform, cuts to social welfare benefits and conscription have all taken a heavy toll on voter support.
And in another headache for Merkel, tens of thousands of nuclear energy opponents took to Berlin's streets last weekend to protest plans to extend the life of reactors well beyond the planned shut-off date of around 2020.
Organisers vow to keep up the pressure with a subject always close to German hearts.
And she surprisingly threw her support behind a massive, unpopular rail project in Stuttgart, which has drawn weekly mass protests.
It is set to become a major issue in a March vote in Baden-Württemberg, where Merkel's conservatives could lose after half a century in power.
"In both cases, (the demonstrators are) not just the usual suspects, and a chancellor or party leader who does not take that seriously ... will not have her job for long," the centre-left daily Süddeutsche Zeitung wrote.
Merkel has also struggled to regain control of a fiery debate on immigration, sparked by the polemical, best-selling new book by Thilo Sarrazin, who created a storm by blasting the integration of Muslims.
Güllner said a free-fall in support for the FDP, and its sharp-tongued leader, Foreign Minister and Vice-Chancellor Guido Westerwelle, was a major problem for Merkel.
"He is the weakest foreign minister in post-war history. He doesn't make mistakes but he doesn't do anything right, he is divisive on domestic issues and he doesn't have the stature for the job," he said.
"At the same time the FDP has not paid attention to what voters really wanted: decent schools, simplification of the tax system, integration of immigrants, cutting red tape."
By any measure, it has been a rough start to her second term as chancellor for the 56-year-old Merkel.
After taking office in October, the coalition was soon wracked by back-biting, feeding doubts that the shy pastor's daughter was unable to wrangle her own ministers.
She earned criticism for what many called foot-dragging during April's Greek credit crisis which imperiled the euro.
May brought an election fiasco in the most populous state, North Rhine-Westphalia, which cost Merkel's alliance its majority in the federal upper house, constricting her ability to pass legislation.
The same month saw the shock resignation of president Horst Köhler over an interview gaffe, amid an exodus of experienced conservatives.
Since the summer break, Merkel has thrown herself into work, promising an "autumn of decision-making" in a tough speech to parliament in which she claimed credit for a robust economic recovery and lower joblessness.
But the influential weekly Die Zeit warned the damage will be tough to repair.
"Not even the economic upturn, that old miracle-worker, can bring back the peace between the people and their government," it wrote.