She made the remarks in a tweet after US President Donald Trump signed proclamations on imposing a 25-percent tariff on imported steel and 10-percent on aluminum amid global dissent.
"The EU is a close ally of the US and we continue to be of the view that the EU should be excluded from these measures," Malmstrom tweeted.
The EU's top trade representative said she would seek clarification from the United States on the issue "in the days to come", adding, "Looking forward to meeting USTR (United States Trade Representative) Lighthizer in Brussels on Sat (Saturday) to discuss."
The EU commissioners on Wednesday gave the political endorsement to a proposal aiming to counter the possible US steel and aluminum tariffs, saying the EU stands ready to react proportionately and fully in line with the World Trade Organisation (WTO) rules once the US measures affect EU's interest. On the hit list of the bloc's countermeasures were said to be flagship US products, including steel, peanut butter, bourbon whiskeys and denim jeans.
"Protectionism cannot be the answer, it never is," Malmstrom told a Wednesday press conference, however, adding that the EU, as a US security partner, still hoped that it could be excluded from the US tariffs.