It was responding to a British parliamentary committee which said the EU naval mission to tackle people smuggling in the central Mediterranean is failing to achieve its aims.
The House of Lords EU Committee says Operation Sophia, named after a baby born on an EU ship that rescued her mother off the coast of Libya in August 2015, does not in any meaningful way disrupt smugglers' boats.
But, on Friday, the Commission responded to the criticism, telling this website that the operation was one of the stories the EU can be proud of.
Responding directly to one of the criticisms, the Commission said it had taken action to tackle the root causes of irregular migration.
In its report published on Thursday, the UK committee said the destruction of wooden boats has forced the smugglers to use rubber dinghies, putting migrants at even greater risk.
Operation Sophia began in 2015 but the report states that "the arrests made to date have been of low-level targets, while the destruction of vessels has simply caused the smugglers to shift from using wooden boats to rubber dinghies, which are even more unsafe".
It says that there are also "significant limits to the intelligence that can be collected about onshore smuggling networks from the high seas".
"There is therefore little prospect of Operation Sophia overturning the business model of people smuggling," according to the document.
It commends the operation is succeeding in carrying out its separate search and rescue obligations.
This is a humanitarian obligation that should be maintained.
However, a naval mission cannot disrupt the business model of people smuggling, and in this sense it is failing.
The report also urges the EU to urgently develop a strategy aimed at tackling the root causes of mass migration.
Committee Chair Lord Tugendhat said, "While 80 smuggler boats have been destroyed by EU naval forces, the sinkings, which take place after migrants are rescued, had simply resulted in smugglers switching from wooden boats to even more dangerous dinghies, which are even more unsafe."
While 50 arrests had been made, they were not the key figures in smuggling networks, the report added.
The smuggling networks operate from Libya, and they extend through Africa.
Without support from a stable Libyan government, the operation is unable to gather the intelligence it needs or tackle the smugglers onshore.
Response to the report was swift, with UKIP migration spokesperson Steven Woolfe MEP saying, "This is very much too little too late. The EU's pitiful attempt to solve the mess caused by German Chancellor Angela Merkel's open invitation to millions is coming apart at the seams.
"The EU's inability to deal with this crisis has played directly into Turkish President Erdogan's hands. He says jump and they say how high; unfortunately for us the Turks are far better at negotiating than David Cameron is."
On Friday, the Commission issued a long statement to this website in defence of the operation.
A spokesperson said, "The report of constitutes an informative contribution to the public debate on Operation Sophia, which aims at disrupting the business model of traffickers in the Mediterranean sea and saving lives. The report includes a number of conclusions and recommendations which we will duly take into account in our ongoing work
"The report applauds the huge contribution of the EU operation to its search and rescue obligations at sea after less than one year of activity. To date, the Operation helped to save more 13,740 lives, among which more than 850 children.
"The mandate is focused on tackling traffickers' networks. After only seven months of operation at high seas, Operation Sophia has contributed to apprehend and transfer to relevant Italian authorities 69 suspected smugglers; the Operation itself has neutralised 114 vessels and contributed to the neutralisation of additional 208 assets."
"This is a substantial achievement in such short period of time."
The spokesperson went on, "The Operation served as a disincentive for traffickers and brought an important contribution to building better knowledge of these criminal networks and making their work more difficult and less profitable. They no longer can operate in impunity in high seas.
"We are now looking at ways for the Operation to be even more effective, building on these achievements.
"The EU is working to make sure that, once conditions are in place, the Operation could swiftly move to the next phase and be able to operate in territorial waters to strengthen its actions against traffickers. As the report rightly says, this depends on receiving an invitation from the Libyan government. We continue to engage with the Libyan authorities on this issue as well as on others."
It continued, "We are working to the possible extension of the mandate of Operation Sophia for one year, and on additional tasks such as the training of coast guard in Libya, to help Libyans take their own responsibility for this issue by tackling the smuggling networks.
"The EU is also planning for a civilian operation to enhance the capacity of Libyan security forces and criminal justice system, also to help a better control of borders. This will require full Libyan ownership if it is to be effective."
The EU says initiative was launched last May "with a view to be important element of a broader EU approach to migration which aims to respond to the immediate need to save lives and address emergency situations, tackle the root causes of irregular migration and fight traffickers."
"The EU has put in place a number of decisions to tackle the root causes of irregular migration and help countries of origin to overcome their development and security challenges.
"For instance, some high level dialogues on migration have been launched with African and Asian partners to better cooperate on the management of migration flows and 16 tailor-made packages are being worked on.
A specific emergency trust fund for stability and efforts to address root causes of irregular migration and displaced persons in Africa worth €1.8bn had been established.
Also, more than €750m worth of projects had been approved in countries such as Niger, Mali, Senegal, Ethiopia, says the EU.
"Therefore," said the spokesperson, "Operation Sophia is one important part of a broader and complementary strategy which has been launched one year ago.
"It is one of the stories of the European Union we can be proud of as stated by EU foreign affairs chief Federica Mogherini on a number of occasions."
In April, the ECR group in Parliament published list of ten priorities that were said to focus on stemming the flows of migrants.
The group called on the European Commission to conduct a full review of existing EU legislation on human trafficking and modern slavery.
It said, At present there are too many loop holes and not enough prosecutions, convictions and meaningful sentencing.
"No corner of the EU should provide a safe haven for these barbaric acts and exploitative crimes. Also, the final phase of Operation Sophia, which is supposed to track down and destroy empty smuggling boats, needs to be initialised with the help of the newly formed Libyan government."
Member states, in March, reaffirmed their commitment to tackling the issue and also welcomed the transition to the next phase of Operation Sophia.