In a survey conducted several weeks before yesterday's killing of 12 people by Islamist gunmen at a French satirical paper, 61 per cent of non-Muslim Germans said Islam had no place in the West.
The figure was up from 52 per cent in 2012, according to the study released by the Bertelsmann Foundation think tank.
In findings that suggested deep anxiety about Muslims in Europe's top economy, more than half -- 57 per cent -- said they felt threatened by Islam, four points higher than in 2012.
Asked about relations between Muslims and non-Muslims in the wake of the Paris rampage, Merkel, who condemned the attack as "despicable", sought to calm fears.
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"We have very good ties with the vast majority of Muslims in Germany. All have been clear in their statements on terrorist attacks," she said.
She acknowledged that there were also "unfortunately some individuals in Germany" who had "joined the jihadists" and said the country must maintain existing security measures.
About four million of Germany's 80 million people are Muslims, mostly of Turkish origin.
"For Muslims, Germany has become home. But they are confronted with a negative image apparently shaped by a minority of radical Islamists," Bertelsmann Foundation Islam expert Yasemin El-Menouar wrote in the study, which also looked at Muslim immigrants' views of Germany.
The authors said that anti-Islam stances could be found regardless of class or education level, but that younger people and those with personal contacts with Muslims showed less prejudice.