This file photo taken December 26, 2011 shows the Pentagon building in Washington, D.C. (Staff/AFP/Getty Images)

President Obama’s most senior advisers convened last month to consider changes to the way the United States provides security aid to foreign nations, as a long-running struggle for control between the State and Defense departments intensifies.

At the heart of the controversy is whether the State Department will retain its historic jurisdiction over security aid, or whether the Pentagon, which Congress has bestowed with increasing autonomy and resources over the past decade, will eclipse Foggy Bottom in taking greater responsibility for engagement with allied nations overseas.

The June 30 meeting of Cabinet officials centered on execution of Obama’s 2013 directive on security assistance, which sought to ensure that the billions of aid dollars the United States provides to allied nations each year are used more effectively.

Adding to concerns at the State Department is a series of proposals in this year’s defense authorization bill, which would give the Pentagon permanent control over certain aid programs and greater flexibility in supporting counterterrorism activities overseas.

The discussions are part of an effort to reform the United States’ unwieldy system for providing assistance to foreign security forces, which includes more than 100 different legislative authorities and accounted for at least $20 billion in U.S. spending in 2015.

State Department officials fear that an expansion in Pentagon control over security assistance would impair diplomatic efforts and move the United States further from the Obama administration’s goal of getting the military out of foreign aid.

Diplomats also say that military-led programs, without adequate input from the State Department, can overlook key human rights or governance concerns and heighten tensions with nations such as China and Russia, because foreign governments see assistance delivered by the U.S. military, rather than civilian agencies, as a potential threat.

“We’ve got to balance the various components of our foreign policy,” said a senior State Department official who, like others, spoke on the condition of anonymity to discuss internal deliberations. “The more money and more authority you move out of traditional accounts we have used for decades to work with our partners, the more you lose the ability to balance.”

After World War II, the United States provided substantial aid to countries such as Egypt, Israel and Jordan, to help those nations build up their own militaries’ powers and, equally, to secure U.S. influence in support of key U.S. goals.

That picture became more complicated after the Sept. 11, 2001, attacks, as Congress authorized new programs to help the U.S. military train and equip Iraqi and Afghan forces and assist allies in combating terrorism. The bulk of new programs were given to the Pentagon to lead, although the State Department retains a veto right over many of them.

Pentagon officials, meanwhile, warn of State Department micromanagement of programs they see not as aid but activities central to U.S. military objectives. They consider certain joint training exercises, for instance, primarily as a vehicle for ensuring the readiness of U.S. troops, rather than a means to build up foreign militaries.

Defense officials say the State Department has used the 2013 order, called a Presidential Policy Directive, to advance an “incredibly broad” definition of what security assistance is, a move that if supported by the White House could increase State Department say over certain programs.

“A lot of what is going on here right now is this disconnect where the State Department has viewed our programs and our authorities and our resources as being in direct competition with theirs, whereas we view them very differently,” one senior defense official said.

The Pentagon has also complained for years that the State Department, which lacks a vast staff to oversee aid programs, is not as fast or nimble as it might be in processing aid proposals. Robust and flexible funding for such programs, defense officials say, will not only help them combat global terrorism threats but will compensate for a shrinking U.S. force.

Gordon Adams, a former White House budget official who is a fellow at the Stimson Center, said the seemingly arcane bureaucratic competition had wide-reaching effects.

“Who owns the ball matters here because it colors the way the U.S. engages overseas,” he said. “If American engagement wears a uniform . . . that’s one form of interaction. If it involves the ambassador and the [U.S. Agency for International Development] and people doing governance work, it’s a different set of missions and there’s a hugely different perception.”

In practice, the Defense Department often executes even programs that are primarily State Department authorities.

The Obama administration has threatened to veto both the Senate and House versions of the defense bill over multiple concerns, including what the White House said were excessive changes to security assistance programs.

Officials said the recent meeting did not produce an immediate resolution to the issue of what programs will be subject to new assistance guidelines.

No matter the final outcome, Michael McNerney, a former Pentagon official who is a scholar at the Rand Corp., said the trend of increasing Pentagon activity with foreign militaries was unlikely to be reversed.

The Obama administration has prioritized efforts to build the skills of partner nations so they, often with U.S. support, can fight militant groups overseas, in part to avoid having to deploy American forces. Many of the initiatives that support that goal are overseen by the Pentagon.

“The toothpaste can’t go back in the tube,” McNerney said. “It’s not realistic to make things the way they were before 9/11.”