The Trump administration voiced plans of issuing US trade sanctions for European companies involved in the completion of new German-Russian and Turkish-Russian natural gas pipelines.
The bloc has called for discussions amid the differences as allies.
Earlier this week, the Trump administration warned companies involved in the projects that they will be subject to US penalties unless they scrap their work.
The move is another step in sparking more tension in the fragile US-European relations.
“I am deeply concerned at the growing use of sanctions, or the threat of sanctions, by the United States against European companies and interests," EU foreign policy chief Josep Borrell said in a statement.
He added that similar attempts had already been made in cases involving Iran, Cuba and the International Criminal Court.
“Where policy differences exist, the European Union is always open to dialogue. But this cannot take place against the threat of sanctions," Borrell said.
“European policies should be determined here in Europe, not by third countries," continued Borrell.