European commissioners, the EU executive's top officials, "expressed their concerns notably because of the draft bill's possible impact on EU energy independence," the bloc said in a statement following talks in Brussels on the matter.
The commission added that it remained "ready to act to protect European interests" if the concerns were not addressed by US lawmakers, repeating a threat made in May by European Commission head Jean-Claude Juncker.
The legislation is aimed at punishing the Kremlin for meddling in the 2016 US presidential election, and Russia's annexation of Crimea.
In an apparent concession, the House modified a provision so the bill only targets pipelines originating in Russia, sparing those that merely pass through, such as the Caspian pipeline that carries oil from Kazakhstan to Europe.
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But Brussels worries the fresh wave of measures could end up penalising European firms that contribute to the development of Russia's energy sector.
"Depending on its implementation, this could affect infrastructure transporting energy resources to Europe," including those transiting through Ukraine, the statement said.
The EU also raised worry over the law's impact on a major natural gas project out of the Baltic states.
Brussels further decried the sanctions bill as a unilateral action by Washington that disrupted previous close cooperation on measures against Russia.
The EU and US imposed the sanctions in the wake of Russia's annexation of Crimea in March 2014 as the Ukraine crisis deepened with the ouster of a pro-Moscow government.
In addition to the Crimea measures, the EU imposed damaging economic sanctions against Russia after the shooting down of Malaysia Airlines flight MH17 in July 2014, blamed by the EU on the rebels.