Speaking in Brussels on Thursday (May26), Wainwright, the agency's director, cited the use made of technology, such as Twitter, by terrorist groups like Islamic State.
He voiced concern at the extent to which such groups make use of technology for their "online propaganda."
He said, "They are very good at it and it's being done on a scale that we have not seen before.
"Groups like IS are very good in their use of social media - IS alone is active on more than 20 platforms, including Twitter where it has, we are told, 5000 accounts.
"The scale is incredible and this is one example of where technology is not always a friend of society and is, in fact, part of the security challenge we face today."
He went on, "But, of course, technology is also a very important part of how we can respond to the threat posed by groups like IS."
Wainwright was a keynote speaker at a full-day conference on how digitisation and technology can support efforts against terrorism and tackling the current migrant crisis.
The 'EU security, migration and borders' conference was organised by Forum Europe and RAND Europe.
On the ongoing efforts to manage the refugee crisis at Europe's borders, Wainright conceded that the EU had been slow to respond to the threat posed by criminal gangs many of whom, he said, were behind the huge influx of migrants heading to Europe.
"Ninety percent of migrants have told us that at least part of their journey was made possible by people smugglers. This is an amazing figure."
Europol has identified 40,000 people-smuggling suspects and it is believed some people smugglers have been making up to €6m from the refugee crisis.
They range from taxi drivers to international smuggling syndicates, said Wainwright.
"There has been an explosion in such criminal activity and people smugglers, keen to exploit a new opportunity, are making a fast buck out of the migrant crisis."
As part of the EU response to this, he pointed out that Europol, based in The Hague, had recently set up a migrant smuggling centre.
The aim, said Wainwright, was to help gather intelligence and "was working very well."
Wainwright, Europol's head since 2009, told the audience the agency had identified 5000 Europeans who had been radicalised by IS of whom about one third had returned to Europe.
Some were in rehabilitation programmes while others had been sentenced to prison.
But he said there were also some who could be plotting terrorist atrocities like those seen in Paris and Brussels.
"They pose a threat we have not seen in Europe for a generation," he declared.
Wainwright, who formerly worked for the UK security services, also said he believes that Europol itself is now being used more effectively by member states than in the past.
"There's been a transformation in the way we are used and trusted."