Gates said it was incumbent upon Nato leaders to "recapitulate to the people of Europe the importance of the Afghanistan mission and its relationship to the wider terrorist threat".
He said: "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.
"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."
The annual conference opened on Saturday in the German city amid a US push for Nato allies to expand their missions in Afghanistan and for an Eastern European-based missile defence system.
In its 44th year, the two-day meeting is used by defence experts and policymakers for frank exchanges.
Gates is one of about 60 senior officials speaking at the conference.
On Friday, entire sections of the business hub of Munich were blocked off near the Bayerischer Hof hotel, where the meeting is being held.
John McCain, the US senator who is a regular at the conference, sent word that he would not attend as he focused on locking up the Republican nomination for the presidency.
He stressed the need for an increased Nato presence in Afghanistan, and for countries to suspend "the debilitating restrictions on when and how those forces can fight".
Sergei Ivanov, Russia's first deputy prime minister, played down renewed tensions with the West in his speech on Sunday.
"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," he said.
"We do not intend to meet this challenge by establishing military blocs or engaging in open confrontation with our opponents."
Last year's conference produced fireworks when Vladimir Putin, the Russian president, accused the US of starting another Cold War by planning to base parts of a missile-defence system in Poland and the Czech Republic.
But writing in Munich's Sueddeutsche Zeitung newspaper on Friday, McCain said "genuine partnership remains open to Moscow, but only if it chooses to uphold its responsibilities to the international community and its own citizens".
He said: "We need a unified Western approach to a revanchist Russia whose leaders seem more determined to chart an old course of conflict rather than join the democratic peace of the West."
Recep Tayyip Erdogan, the Turkish prime minister, who opened the conference on Saturday, said his country will continue its fight against Kurdish separatists in northern Iraq "until we win".
He said the fight against the PKK was part of the world's war against terrorism.
|Erdogan spoke on Saturday on Turkey's|
foreign policy and security interests [AFP]
"Let me put it very clearly ..." he said.
"We are going to continue until we win."
Erdogan said: "Turkey is not interested in one inch of territory that belongs to Iraq.
"In fact, Turkey is the largest supporter of the territorial integrity of Iraq."
The previous day, Boris Tadic, the pro-Western Serbian president, addressed the opening dinner, telling guests that accepting a declaration of independence from Kosovo could have serious ramifications.
Kosovo's ethnic Albanian leadership has said a declaration could be made within days.
"Should Serbia be partitioned against its will - which is what the imposed independence of Kosovo is in truth - it could in turn result in the escalation of many existing conflicts, the reactivation of a number of frozen conflicts, and the instigation of who knows how many new conflicts," Tadic said.