"Broadly speaking, when it comes to America's engagement with the rest of the world, it is important that the military is -- and is clearly seen to be -- in a supporting role to civilian agencies," he said.
"Our diplomatic leaders -- be they in ambassadors' suites or on the State Department's seventh floor -- must have the resources and political support needed to fully exercise their statutory responsibilities in leading American foreign policy," he said.
He said he sensed bipartisan support in Congress for strengthening the civilian foreign affairs budget.
"It has become clear that America's civilian institutions of diplomacy and development have been chronically undermanned and underfunded for far too long -- relative to what we traditionally spend on the military, and more importantly, relative to the responsibilities and challenges our nation has around the world."
Gates' speech was prepared for delivery to the US Global Leadership Campaign, a group that brings together representatives of private humanitarian relief organizations and corporations.
It comes amid debate over how aggressively the US military should take on nation building tasks that have traditionally fallen to diplomats and civilian aid experts.
Gates said he believes future security threats are more likely to emanate from poor or failing states than from rising powers.
US military thinking likewise has shifted from focusing on direct military action to shaping the security environment to prevent the need for military intervention, he said.
"Overall, even outside Iraq and Afghanistan, the US military has become more involved in a range of activities that in the past were perceived to the exclusive province of civilian agencies and organizations," he said.
"This has led to concern among many organizations -- including probably many represented here tonight -- about what's seen as a creeping 'militarization' of some aspects of America's foreign policy," he said.
"This is not an entirely unreasonable sentiment."