The new laws, agreed in 2011, impose higher penalties on offenders, make it easier to prosecute across borders within the bloc and give better protection to victims.
Only six countries have implemented the new legislation so far, the Commission said.
Trafficking victims are typically women and they are predominantly forced into sexual slavery, but also hard labor and criminal activity. Some have their organs removed.
Information released by the EU executive showed 23,632 people were identified or presumed victims of trafficking in the EU over the 2008-2010 period, increasing by 18%. Nearly 21 million people worldwide are victims of human trafficking, according to 2012 statistics from the International Labor Organization.
"What we know is probably only the tip of the iceberg," said Cecilia Malmström, the EU commissioner for home affairs.
"I am very disappointed to see that, despite these alarming trends, only a few countries have implemented the anti-trafficking legislation and I urge those who have not yet done so to respect their obligations."
Most of the victims identified were citizens of Romania and Bulgaria, the two poorest members of the bloc. Neither country has implemented the new laws.
EU governments which do not implement common rules can face legal action and fines.