Speaking at a conference on anti-Semitism, the Dutch official said, "The legislation is there. It is EU-wide, it is clear. It makes serious manifestations of racism and xenophobia punishable by means of criminal law.
"But still it is not enforced everywhere, for everyone. Let's not make this mistake to turn this into an integration issue. This is a penal issue. This is about law; this is about applying the law. And it should be applied more widely in our member states."
As an example, he said that only 13 out of 28 member states have criminalised Holocaust denial.
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He said this was one reason why the Commission is "pushing and we will keep pushing - using all our powers - to make sure that these rules are correctly translated into national legislation and correctly enforced."
He added, "That is the basic minimum."
Enforcement of laws on anti-Semitism and anti-Muslim hatred speech also extends to the internet, Timmermans told the conference.
"The internet is no legal black hole, no free haven for hate speech. So at EU level, we've stepped up our talks with Google, Facebook, Twitter and Microsoft - the set-up is partly inspired in fact by the German task-force model.
"So far the talks are tough but encouraging. What we are asking IT platforms is that when they examine content flagged as hate speech they do not hide behind US law but abide by EU law and national laws that apply.
"When the alert comes from public authorities or trusted watchdogs, it has already been vetted: there is no reason why hate speech cannot be taken down within hours. Not days or weeks.
"Platforms make large profits. They cannot leave the responsibility for countering hate speech to charities, public authorities and taxpayers, so we expect them to shoulder their share in supporting those who flag and develop counter-narratives."
He cited a recent event which happened in his home country, the Netherlands, "where mosques received pamphlets with Nazi symbols, threatening to hurt them, and a Molotov cocktail was thrown against the wall of a mosque.
"It was a Jewish community that spoke up first to condemn this. The Jewish community in the Netherlands understood first that if one minority is a target, the other minorities will soon follow. And there is no pitting one minority against the other in society. We all suffer under this attitude of singling out minorities and scapegoats, something we have done so often."
He said that incidence of anti-Semitism were happening again.
"Jewish children leaving public schools for fear of harassment, teachers no longer daring to teach the Holocaust in a multicultural classroom, synagogues heavily guarded, students warned to hide their kippahs beneath baseball caps for fear of being knifed on the streets."
Meanwhile, EU governments have been urged to adopt a working definition of anti-Semitism.
In 2013 the EU's Agency for Fundamental Rights dropped a definition of anti-Semitism from its website, eliciting harsh criticism from Israel and Jewish communities worldwide.
The call was made by U.S State Department Special Envoy to Monitor and Combat Anti-Semitism Ira Forman.
Citing several occasions in which apparently anti-Semitic incidents were downplayed as being merely anti-Israel, including the scrawling of swastikas in Sweden and the firebombing of a synagogue in Germany, Forman said that it is vital to "define anti-Semitism clearly to more effectively combat it."