His comments come despite the softening of the bill after the EU had expressed earlier concerns.
Juncker was speaking after US President Donald Trump's signature of the 'Countering America's adversaries through sanctions' Act, which restricts US investment and business dealings with Russian energy schemes and companies.
Juncker, responding to the new measures, said, "I stated at the G7 summit in Taormina, Italy, and at the G20 summit in Hamburg, Germany, that if the Americans proceeded [with the adoption of new sanctions], we would be ready to react adequately in a matter of days.
"As a result, a significant proportion of the intended sanctions against Russia have been dropped. Moreover, the US Congress has now also committed to only apply sanctions after the country's allies are consulted. And I do believe we are still allies of the US", Juncker said.
He said European interests can thus be taken into account in the implementation of any sanctions and, if not, the Commission reserves the right to take adequate measures.
His intervention comes amid reports that European commercial interests could have been harmed by US sanctions against Russia.
"If the US sanctions specifically disadvantage EU companies trading with Russia in the energy sector the EU is prepared to take appropriate steps in response within days.
"We are prepared", Juncker said. "We must defend our economic interests vis-a-vis the United States. And we will do that."
The EU, a Commission spokesperson said, is maintaining its own sanctions against Russia.
"However, in order to fully implement the Minsk agreements, the G7 must unanimously agree on the sanctions, with close cooperation between the allies.
"The US bill could have an unintended impact on EU interests relating to energy supply security. The sanctions would affect energy transport and the maintenance of pipeline systems in Russia which supply the Ukrainian gas transit system. The new US sanctions could also impact EU efforts to further diversify the energy sector, particularly in the Baltic.
Reacting to the news, Russian Prime Minister Dmitry Medvedev said the measures represented a "full-scale trade war."
While the US measures also place restrictions on dealings with Iran and North Korea, in Russia's case they are designed to form a punitive response to Russia's alleged interference in the 2016 US elections and actions in Ukraine.
Despite signing the Act, Trump appended a critical statement calling its measures "deeply flawed," an action seized on by Medvedev as evidence of Trump's lack of power. Nevertheless, Medvedev said, "The sanctions regime has been codified and will remain in effect for decades unless a miracle happens."