The planned free trade agreement has come under political scrutiny in recent weeks, amid protests by farmers who say they are being undercut by cheap imports from countries that do not uphold the EU's strict environmental standards.
"The Commission assessment is that the conditions for the conclusion of the Mercosur agreement are not met," Sefcovic told the European Parliament on Wednesday.
A Commission spokesman told Reuters negotiations on the deal were continuing.
The European Union and the Mercosur bloc of Argentina, Brazil, Paraguay and Uruguay have been in talks for years over the accord, with the EU pushing in recent negotiations for stronger assurances on climate change and deforestation.
France has repeatedly expressed reservations about the EU-Mercosur deal and President Emmanuel Macron last week told Brussels it would be impossible to conclude negotiations under the current conditions.
With farmers staging massive protests in France and polls pointing to gains by the far right in European Parliament elections in June, Macron is under pressure to assuage farmers who are angry over rising costs and cheap food imports.
EU governments and the European Parliament need to approve any trade deal the Commission has reached.
(Reporting by Kate Abnett, Bart Meijer; Editing by Sharon Singleton)
By Kate Abnett
