Angela Merkel’s political fortunes are increasingly hostage to events in distant Afghanistan just weeks after her triumphant re-election as German chancellor at the head of her coalition of choice.

Seven weeks into a second term, Merkel has lost one of her most loyal ministers over an airstrike that killed civilians and has come under mounting pressure to say what she knew about the embarrassing pre-election incident in an unpopular war.

At the same time, US President Barack Obama is pressing for more soldiers from Germany, which has the third biggest NATO contingent in Afghanistan with close to 4,500 troops. “Afghanistan is the government’s biggest foreign policy headache and it’s increasingly becoming a major domestic one too,” said Dietmar Herz, a political scientist at the University of Erfurt. “The year 2010 will be very difficult for Merkel.” Already struggling to forge an agreement on planned tax cuts within her conservative bloc, Merkel has faced a growing barrage of fire from left-wing opposition charging that she has the blood of Afghan civilians on her hands. On Wednesday, a parliamentary investigation into the Sept. 4 strike in Kunduz — which Kabul says killed 69 insurgents and 30 civilians — will began to shed light on what her government knew about the killings and whether it deliberately suppressed details of the attack before a Sept. 27 federal election.

Opposition lawmakers are demanding Merkel testify at the hearings.

Having to defend the army to a skeptical public would be a fresh blow to Merkel, who had hoped governing Germany would get easier after winning the election allowed her to form a new coalition with her preferred partners, the Free Democrats (FDP).

However, her conservatives quickly became embroiled in spats on two fronts with the FDP over plans to cut income tax and a controversial new museum focusing on the plight of Germans forced out of Eastern Europe following the defeat of the Nazis.

With polls showing voters are against the German military deployment, Herz said a rejuvenated opposition was warming to the task of hammering Merkel on the Afghan front, and even some senior conservatives were reluctant to commit more forces. One compromise under discussion would be to raise Germany’s police presence in the country without sending more soldiers.

Merkel has less room to build consensus without the broad parliamentary majority afforded by the “grand coalition” of conservatives and Social Democrats (SPD) in her first term, putting her under more pressure to decide matters herself.

“We’re now faced with the question of what sort of inner compass Merkel really has to lead Germany forward,” said Uwe Andersen, a political scientist at the University of Bochum.

The Sept. 4 strike on two tankers in Kunduz carried out by a US warplane at the request of German forces claimed the scalp last month of Franz Josef Jung, a staunch ally of Merkel in the Cabinet who was defense minister at the time. Opposition politicians are now calling on Jung’s successor Karl-Theodor zu Guttenberg to resign. They argue he knew about the civilian deaths earlier than he admitted, and forced out the head of Germany’s armed forces to draw a line under the affair. “If it comes out he did know more than he said and sacrificed the head of the armed forces, it’s hard to see how he could stay in office,” said Andersen at Bochum University.

Adding to the furor have been reports that the German officer who called in the air raid had deliberately sought to kill enemy combatants — prompting accusations that this overstepped Germany’s Afghanistan mandate. Jan van Aken, a lawmaker in the leftist opposition, said targeting people was “an unprecedented breach of taboo” in postwar Germany and called the strike “Merkel’s Kunduz-gate”.

Until Guttenberg took office, Berlin avoided referring to the Afghan conflict as a war. Political scientist Andersen said Merkel had to become more open about the deployment. “Because of Germany’s history, politicians have downplayed it,” he said. “But reality catches up with you in the end.” Recent polls have shown support for the opposition on the up, raising the chance Merkel’s conservatives may lose power in an election next year in North Rhine-Westphalia, a traditionally left-leaning state where more than one in five Germans live.