BRUSSELS -- Prime Minister Justin Trudeau revelled in a long-awaited moment Sunday -- signing Canada's free trade deal with the European Union, but not before recognizing the challenges ahead to bring it fully into force.

Trudeau expressed hope that the so-called provisional application of the deal -- approval only by the Canadian and European parliaments but not Europe's 28 states and myriad regional governments -- might happen within months.

That, said Trudeau, would result in 98 per cent of the deal coming into force. That's much higher than the 90-per cent estimate that most European and Canadian officials have said would accompany provisional application of the Comprehensive Economic and Trade Agreement, known as CETA.

Trudeau had initially expected to sign the deal in Brussels days ago, but the restive Belgian region of Wallonia nearly killed it because its opposition to the pact's investor-state dispute settlement mechanism gave it a veto under Belgium's complicated constitution.

After seven arduous years of negotiation, Trudeau joined presidents of the European Council and European Commission, Donald Tusk and Jean-Claude Juncker, and signed the massive 1,600-page pact and its accompanying strategic partnership agreement.

The road to full ratification remains long. After Trudeau and his EU counterparts took a moment Sunday to revel in the milestone, the prime minister was willing to acknowledge it would take more than ceremony to fully ratify the deal.

"The work is only just beginning right now," Trudeau said.

"It's not just signing the accords, as difficult and important as that is. It's about the followup, that we continue to demonstrate and give tools to small and medium sized businesses."

Trudeau didn't betray a hint of bitterness towards the socialist regional government of Wallonia, led by Paul Magnette, which picked up the anti-CETA baton that had flourished previously in France, Germany and Austria.

The latest obstacle to CETA was removed Friday when Wallonia officially voted to withdraw its opposition to the deal, paving the way for Trudeau's trip.

"The fact that throughout people were asking tough questions of a deal that will have a significant impact on our economies, and giving us the opportunity to demonstrate that that impact will be positive, is a good thing," Trudeau said.

"That is what a democracy is: we need to have a whole chorus of different voices, able to share their concerns."

Trudeau also praised the support he received from the government of Quebec's Liberal Premier Philippe Couillard, who was in Brussels along with one of his predecessors, Jean Charest, one of CETA's early boosters.

International Trade Minister Chrystia Freeland called it a great day for Europe.

More than a week ago, Freeland walked out of talks in Belgium, saying it appeared the EU was incapable of signing an agreement.

"OK we did it!" she blurted out during a photo opportunity following the signing ceremony.

The deal's supporters say it will boost trade by billions through cuts in tariffs across a broad swath of sectors including agriculture, pharmaceuticals and the auto industry.

But opposition among anti-trade activists and left-wing political parties in some European countries has been fierce and nearly blocked the deal. On a sleepy Sunday morning in the largely shuttered EU capital, Trudeau's entourage was greeted by a small but vocal group of protesters at the European Council.

Trudeau acknowledged the discontent but said political leaders had to work to overcome it.

"That leadership that we were able to show between Canada and Europe is not just something that will reassure our own citizens but should be an example to the world of how we can move forward on trade deals that do genuinely benefit everyone," Trudeau said.

With the Liberals and Conservatives both favouring the deal, its approval will sail through Parliament.

But Europe is another matter.

The European Parliament must approve CETA. Before leaving Brussels, Trudeau met with its leader, Martin Schulz, the German social democrat.

Trudeau thanked Schulz for his leadership on CETA and said he wanted to "thank him in advance" for the work he will do to get it "ratified quickly."

The European Parliament's approval is expected by many to come in early 2017.

But the deal must be ratified by the EU's 28 countries and several more smaller regional governments such as Wallonia. That process could take years, and could be derailed.

Gus Van Harten, an Osgoode Hall law professor who specializes in trade, said he believes the European Parliament will likely approve the deal, but the foreign investor protection mechanism will likely pose problems in the future. That's because national and regional governments have the ability to block it, ending the provisional application of the deal.

"The inclusion of the foreign investor protection system in the CETA was a dubious decision and political gamble from the start, and it has now blown up in a lot of faces," said Van Harten. "CETA as a whole remains in jeopardy regardless of signature."

Sunday was not the first time Brussels witnessed the pomp and circumstance of a CETA signing ceremony.

In October 2013, former Conservative prime minister Stephen Harper flew to Brussels with great fanfare and signed an agreement in principle with European Commissioner Jose Manuel Barroso.

In September 2014, Harper hosted Barroso and at another signing ceremony in Ottawa to mark the end of negotiations.

But while they were celebrating in Ottawa, the seeds of discontent with the investor protection chapter were flowering in Germany. After the Liberals won power a year later, German Vice Chancellor Sigmar Gabriel -- a major opponent of that chapter -- would find himself working with Freeland to strengthen that section of the agreement.