The new measures, approved by the US Senate on Thursday, include a threat to penalise companies that provide "goods, services, technology, information or support" for the construction of Russian energy export pipelines.
Berlin noted that this would directly impact European companies involved in the construction of the controversial Nord Stream 2 pipeline which would pump Russian gas under the Baltic Sea directly to Germany.
"It is strange that in the sanctioning of Russia's behaviour, with regards to the US elections for instance, the European economy should become a target of American sanctions," said Chancellor Angela Merkel's spokesman Steffen Seibert.
He added that Merkel shared the concerns raised by German Foreign Minister Sigmar Gabriel and Austrian Chancellor Christian Kern, who charged in a joint statement Thursday that the measure brings a "completely new and entirely negative quality to European-US relations".
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They also accused Washington of using the sanctions to squeeze Russian gas supplies out of Europe in favour of US energy exports.
Separately, France's foreign ministry called on Washington to respect the need for coordination with its European allies before deciding new sanctions.
"For several years, we have stressed the difficulties that extra-territorial legislations could generate," said a spokesman at the French foreign ministry, referring to measures that could have a spillover effect to countries besides the one directly sanctioned.
Russian energy giant Gazprom is building Nord Stream 2 in cooperation with Anglo-Dutch Shell, Germany's Uniper and Wintershall, Austria's OMV and France's Engie.
The project bypassing conflict-torn Ukraine and also Poland would double the flow of the Nord Stream pipeline currently linking Germany and Russia.
But it has sparked criticism within the EU, with members including Italy and Poland accusing Germany of selfishly seeking a reliable energy supply route from President Vladimir Putin's Russia while pressuring other countries to back sanctions against Moscow over the crisis in Ukraine.
But Germany's Gabriel and Austria's Kern said Washington's intention was purely economic.
"The aim is to secure jobs in gas and oil industries in the US," said Gabriel and Kern.
"Political sanctions should not be mixed up with economic interests," they warned, stressing that "Europe's energy supply is Europe's business and not that of the United States".
"We decide who delivers energy to us and how, according to rules of openness and economic competitiveness," said Gabriel and Kern.
Gazprom's vice president Alexander Medvedev also charged that the US had a vested interest in hurting the project.
"With regards to the introduction of sanctions, they don't hide the fact that it's an anti-competition tool to favour US gas deliveries in Europe," he said according to Russian news agencies.
The US bill as originally introduced was exclusively about slapping new sanctions on Iran. But lawmakers attached a bipartisan amendment on Russia to it early this week.
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