The EU executive called on Malta to find the "barbarous" assassins of a journalist being buried on Friday and resolve "potential structural problems" with the rule of law on the island.
Daphne Caruana Galizia, Malta's best-known investigative journalist, was killed last month when a powerful bomb blew up her car, in a case that stunned the small Mediterranean island.
In the European Commission's strongest comments yet on concerns about systemic democratic failings in the EU's smallest state, First Vice President Frans Timmermans said Malta should leave "no stone unturned" in the hunt for her killers.
"The eyes of Europe are on the Maltese authorities," wrote Timmermans, a former Dutch foreign minister who as Jean-Claude Juncker's deputy oversees Brussels' efforts to ensure member states respect democratic and judicial standards.
"We want those directly and indirectly responsible for this horrible murder to be brought to justice. And we want the investigations to run their full course, so that any other related wrong-doings that may emerge can also be prosecuted and potential structural problems be resolved," he added.
He said democracy was at stake on an island where the prime minister, his wife and other senior figures in government and opposition were pursuing journalists for libel over allegations of corruption and international money laundering.
"This will not happen in Europe. Not on this Commission's watch," Timmermans said.
The European Commission said in a separate statement Juncker condemned the attacks in the strongest possible terms. "The right of a journalist to investigate, ask uncomfortable questions and report effectively, is at the heart of our values and needs to be guaranteed at all times," the statement said.
Prime Minister Joseph Muscat says everything will be done to find Caruana Galicia's killers. His government announced a one million-euro reward and protection for anyone providing information to help identify whoever was behind the murder.
The Commission has limited power to intervene directly in member states and officials say there is no "European FBI".
It has applied largely moral pressure on the likes of Hungary and most recently Poland to reverse proposed laws that it sees as breaching EU treaties by curbing judicial, media or other freedoms.
It has warned that it could seek to suspend Poland, but this would require support from all member states - something the Commission sees as difficult given resistance among governments to allow the EU executive such power to intervene.
The Commission does also have powers to fine states for breaches of EU legislation. (Reporting by Alastair Macdonald, writing by Robert-Jan Bartunek, Editing by William Maclean)