Cecilia Malmstrom’s words come after the US president slapped tariffs on steel and aluminium imported from the European Union, Canada and Mexico.
Donald Trump said the 25% tariff on steel and 10% tariff on aluminium was in the US’ national interest, but EU leaders have described the move as “protectionism” and “illegal”.
The tariffs are expected to affect EU exports that were worth €6.4bn (£5.6bn) in 2017.
Ms Malmstrom said: “This is very unfortunate… because it will cause a lot of damage to our steel and aluminium industry.
“It’s unfortunate because the motivation behind this, the Section 232 that the Americans are using – internal security – is not relevant. It is pure protectionism.
“European steel and aluminium exports to the United States cannot be seen as a threat to their internal security.
“It is unfortunate because this is further weakening the transatlantic relations and it also increases the risk of severe turbulence in the markets globally.”
She added: “This is something that has been imposed by the US, we didn’t ask for it.”
“We have no intention to escalate this, the door for dialogue is always open…the ball is in (the US’s) court.”
The EU has already started a case against the US at the World Trade Organisation in Geneva, although this route may take many months to reach a conclusion.
In 2002, the EU brought a previous steel dispute with the US to the WTO and 18 months passed before it was finally settled in the EU’s favour.
The EU is also planning retaliatory tariffs on US steel and food in the coming weeks, once the cost of the US tariffs becomes clear.
Canada has already hit back, announcing retaliatory duties on American goods worth up to Can$16.6bn (USD$12.8 bn).
Mr Trump responded to this on Twitter, writing: “Canada has treated our agricultural business and farmers very poorly for a very long period of time.
“Highly restrictive on trade!
“They must open their markets and take down their trade barriers!
“They report a really high surplus on trade with us. Do timber and lumber in the US?”
After the measures were announced on Thursday, the UK’s international trade secretary Liam Fox also dismissed Mr Trump’s claim that the tariffs were for security reasons.
Dr Fox branded Mr Trump’s decision as “just protectionism” and said: “We absolutely do not rule out counter measures.”
UK steel bosses have also expressed fears of the effect tariffs will have on the industry, saying that the US move is a “big mistake”.
Ms Malmstrom also announced the EU will be taking China to the WTO over alleged intellectual property practices, which bar market access to overseas companies without the granting of sensitive technology to Chinese firms.
She said: “If players in the world don’t stick to the rule book the system might collapse.
“That is why we are challenging the US and China at the WTO and it demonstrates that we are not choosing any side.”