When Turkey shot down a Russian jet on Tuesday, Nato was facing its worst fear: a direct confrontation with the Russian military. The problem on Nato's southern border is much bigger than this one incident; the new Russian base near Turkey presents a larger strategic challenge for the alliance that, if ignored, could lead to ongoing clashes.

Just days ago, Nato military committee chairman Petr Pavel, the top military adviser to Nato's secretary-general, warned me about the long-term implications of the new Russian airbase in Latakia, Syria.

The Czech general did not know then that the Russian presence in Syria would cause an international crisis so soon. But he already knew that Nato needed to figure out a comprehensive policy to push back against Russia's new base.

He said the base is not just intended to prop up the regime of President Bashar al-Assad in Syria.

"Of course, it is one of the objectives of Russian activities in the Middle East, not just to support Assad's regime but also to get their forces into the area, have presence and, through this presence, exert some influence," Gen Pavel told me at the Halifax International Security Forum.

He said the base in Latakia was part of a broader Russian policy to increase its permanent military presence on several of Nato's borders. This installation serves the Russian agenda in Syria while also attempting to deny Nato access to this area.

"There are different ways Nato can react," Gen Pavel said. Facing Russia's attempt to impose anti-access, area-denial capability near Turkey, he said, "the most brutal way of how to resolve the issue… is to suppress it".

But using military assets to challenge Russia's new protected zone around its base would take a lot of resources and carries risks of further confrontation, he warned. He would rather that Nato use less "brutal" tools to bear against Moscow.

"We can use different kinds of pressures, starting from political, diplomatic, economic and also military in other areas, rather than pushing through the wall," he said.

Gen Pavel predicted days ago that Nato would have to meet to discuss the Russian presence in Latakia soon. He was right. Nato held an emergency meeting on Tuesday to discuss the Turkish downing of the Russian jet.

The Turkish government issued a statement saying the Russian jet entered Turkish airspace over the town of Yayladagi, was warned 10 times in five minutes, and then was shot down.

The Turkish Foreign Ministry said the issue was not only Russian incursion into Turkish airspace.

The Turkish government had been protesting against what it says were Russian attacks on Turkmen villages on the Syrian side of the border, whose citizens Ankara feels a responsibility to protect because of their Turkish heritage.

Russian President Vladimir Putin reacted angrily to the incident and called the Turkish government "accomplices of terrorists", accusing Ankara of supporting radical Syrian rebel groups.

Russian Foreign Minister Sergei Lavrov cancelled a planned Wednesday visit to Turkey. Syrian rebels reportedly used a US-provided TOW anti-tank missile to shoot down a Russian rescue helicopter as well.

The clash between Russia and Turkey is destabilising, but the real destabilising move was Mr Putin's decision to place a new power-projection and access-denial base just kilometres from a Nato country without any consultation.

Nato chose not to deal with that dangerous situation for months. Now the alliance has no choice.

BLOOMBERG VIEW