Washington is trying to persuade European allies such as Germany, France, Italy, Spain and Turkey to send more combat troops to fight the Taliban in southern Afghanistan.
Nato's UN-mandated International Security Assistance Force (ISAF) in Afghanistan has grown from 16,000 to 43,000 troops in the last two years, but commanders have been calling for more soldiers.
Public supportThe force is primarily made up of US and British troops, and other countries have been reluctant to increase their commitment due to a lack of public support.
"Many Europeans question the relevance of our actions and doubt whether the mission is worth the lives of their sons and daughters. As a result, many want to remove their troops," Gates said.
"So now I would like to add my voice to those of many allied leaders and speak directly to the people of Europe: The threat posed by violent Islamic extremism is real - and it is not going away."
German, Spanish and Italian contingents in Afghanistan only take part in reconstruction and civic affairs missions, while Britain, Canada and the US carry out dangerous combat missions.
Gates said on Sunday that such a system was unfair.
"In Nato, some allies ought not to have the luxury of opting only for stability and civilian operations, thus forcing other allies to bear a disproportionate share of the fighting and the dying," he said.
The two-day meeting in Munich, which is now in its 44th year, is used by defence experts and policymakers for frank exchanges.
Missile row
Gates did not touch on the recent disagreement between the US and Russia over plans for a missile system in Poland and the Czech Republic, but Russia's first deputy prime minister played down tensions in his speech.
"I am sure that everyone here clearly realises that the process of Russia's revival objectively combines our ambition to occupy an appropriate place in world politics and commitment to maintain our national interests," Sergei Ivanov said.