The US leader has rattled allies by refusing to rule out using military force to take over the autonomous territory of fellow NATO member Denmark.
Trump says controlling the mineral-rich island is crucial for US national security given the rising threat of Russia and China in the Arctic.
NATO has sought to deflect Washington's interest in Greenland by emphasising steps it is taking to bolster security in the region.
A NATO spokeswoman said Rutte spoke with Rubio "on the importance of the Arctic to our shared security and how NATO is working to enhance our capabilities in the High North."
Danish Prime Minister Mette Frederiksen has warned that an armed US attack to take Greenland could spell the end for the 76-year-old Western military alliance.
But the head of NATO's forces in Europe, US General Alexus Grynkewich, said Friday the alliance was far from being in "a crisis", following President Donald Trump's threats.
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