Speaking in Parliament on Wednesday, John Gatt-Rutter, of the European external action service (EEAS), said this was the "biggest security issue" currently facing Europe.
He also called on the EU to devise a "more ambitious" policy for dealing with the issue.
Gatt-Rutter, who heads the division for counter terrorism at the EEAS, was speaking at a public hearing on the international efforts to combat Isis.
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He told the packed meeting that the successes of the US-led coalition in tackling Isis had resulted in the terror organisation suffering a "shrinking physical space."
But this, he warned, meant that foreign fighters who had left Europe to join Isis were now likely to head back to member states in the coming months and years.
A report released by the Paris-based Centre for the Analysis of Terror recently revealed that nearly 7000 foreign fighters from European countries have joined terror groups in Syria and Iraq since 2013.
According to the report, about 2200 French citizens or residents are engaged in Syrian-Iraqi terror networks, including 700 who are in either Syria or Iraq.
Nearly 70 per cent of the 7000 European terrorist fighters come from either France, the UK, or Germany.
The top three countries were followed by Belgium, Sweden, and Austria as the countries with the highest number of nationals or residents leaving for terror networks in Syria and Iraq.
The report said that about 1500 of those who left for Syria and Iraq have returned to the EU countries.
Gatt-Rutter told MEPs, "How we deal with this in Europe is the key question. We need to devise a more ambitious policy which involves carefully vetting these people and assessing the level of threat they pose to us.
"Some might be rehabilitated but others, of course, will be beyond the pale and beyond rehabilitation. How we deal with these is probably the number one security issue we currently face."
The official added, "The EU has a key role to play here with various measures including better information exchange between member states.
"The coalition is working well at present but the threat remains very real and that is why we need to step up measures to counter Isis and other such groups."
His comments come after it recently emerged that the European Union will from now on be able to freeze assets and impose travel bans on people associated with the Isis and Al-Qaida jihadist groups, even if they are not on UN blacklists.
The move, agreed by the Council on 20 September is primarily targeted against EU nationals.
In particular, people trying to travel to Syria could be stopped from leaving in the first place, or from coming back to another EU country besides than the one they hold the passport of. It will also become easier for EU countries to prosecute their own nationals for terrorist-related activities.