The meeting came just a day ahead of the planned introduction of a parliamentary motion to extend and expand Canada's combat mission against extremists in Iraq — and possibly Syria.
Sources tell The Canadian Press that Harper will introduce the motion Tuesday morning.
Stoltenberg, a former prime minister of Norway who became the alliance's secretary general last year, said the alliance is engaged in the troubled region despite having no formal role in the U.S-led coalition.
"NATO is also doing lots to fight and to try to work with partners in the region to stabilize them," Stoltenberg said during a photo-op with Harper, Defence Minister Jason Kenney and Foreign Affairs Minister Rob Nicholson ahead of the meeting.
"Because if you are able to make the Middle East more stable, we will become more secure."
Stoltenberg praised Canada's contribution in Iraq and to NATO's reassurance missions in eastern Europe, which have included fighter jets, the deployment of a frigate and ground troops on a training exercise.
In an interview last fall, the alliance's top military commander said it was widely expected NATO would be called upon to contribute to a mission to train Iraqi security forces the way it did in Afghanistan.
A NATO official, speaking on background late Monday, said that it has received a request for "defence capacity building" from the government in Baghdad, which the alliance is still reviewing.
Whether that takes the form of a full-fledged training mission has yet to be decided. Capacity building could run from working with Iraqi ministries right up to field training.
The two leaders were expected to discuss the phenomenon of foreign fighters travelling overseas to join ISIL, swelling the ranks of the extremist group and forcing the hand of allied nations in confronting the threat.
It is unclear how much of the talk involved international pressure to convince Turkey, a major NATO ally, to take more decisive action to seal its border with Syria, a major transit point for foreigners wanting to join the fight.
In a statement issued after the meeting, Stoltenberg's office said the discussions were "focused on the implications of Russia's aggressive actions against Ukraine" as well the crisis in the Middle East.
Monday's get-together happened one day after U.S. Gen. Philip Breedlove, NATO's supreme commander, warned that Russian arms are still getting into eastern Ukraine, despite a shaky truce. Breedlove's comments focused attention back on the issue of whether Washington and its allies are prepared to ship lethal weapons to bolster President Petro Poroshenko's government.
Canada, which has sent two shipments of non-lethal aid, has been largely silent on the issue of whether it would participate in such an arrangement.
Stoltenberg was also expected to update Harper on NATO's plan to create a beefed-up rapid reaction force of 30,000 troops and a separate, smaller ultra-high readiness force — both of which would be available to respond to a crisis in Europe.
National Defence has committed troops, planes and ships to a massive exercise this year to test those forces, but the alliance is looking for a commitment from members such as Canada for troops, transports or cash to support the structure.
One sore point in the discussion could very well have been over money.
NATO — led by the U.S. and Britain — was leaning on members at the leader's summit last fall to boost defence spending to meet its benchmark expectation of two per cent of gross domestic product.
Canada spends one per cent of its GDP on defence.
Harper's office, in background documents, pointed out that Canada is spending $180 million this year supporting the alliance's budget, making the country the sixth largest financial contributor to NATO.
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