“I'll say this very carefully,” Merkel said at a convention of the Federation of German Industries (BDI) in Berlin. “The fact is that if we were negotiating with Russia, it would probably only cause half the debate - that should give us pause for thought.”
The Chancellor then added that it is necessary to ask whether the debate is really about the free trade deal TTIP or about something else entirely, implying that anti-Americanism was the true motive for opposition, Die Zeit reports.
The European Union and the United States began negotiating the Transatlantic Trade and Investment Partnership (TTIP) in 2013, aiming to create the world's biggest free trade market of 850 million consumers.
But the talks have become bogged down amid widespread belief in Europe that the deal would undercut the 28-nation bloc's standards in key areas such as health and welfare.
Some of the sharpest criticism has come from Germany, where around 160,000 rallied in seven cities in September against the deal, as well as against a separate free trade deal with Canada, called CETA.
Exporters are in favour of the deal as it promises lower tariffs, less red tape and a wider base of consumers for their goods.
But in Europe, consumers fear it would ride roughshod over the EU's labour market and environmental standards, and would bring about more outsourcing which would lead to job losses.
There are also concerns over plans for a special court to hear cases by companies against governments over breaches of regulatory issues, which opponents see as giving firms a veto over public policy.
Merkel's Vice-Chancellor Sigmar Gabriel, leader of the Social Democrats (SPD), has described the deal as having "de facto failed", blaming the US for an unwillingness to compromise.
But, speaking to the BDI convention, Merkel said that the negotiations between the EU and the US should “be pushed ahead for as long as possible,” adding that “with good political will one can achieve a lot.”
A new round of talks is due in October with US President Barack Obama hoping a deal can be concluded before he leaves office in January.