IN HIS recent address at West Point, President Obama doubled down on his administration’s strategy of combating terrorism and other security threats through “partnerships” with other armies. Describing the strategy as an alternative to “invading every country that harbors terrorist networks,” the president said he would ask Congress to appropriate $5 billion for a Counterterrorism Partnerships Fund to “train, build capacity and facilitate partner countries on the front lines.”

There’s nothing particularly new about Mr. Obama’s initiative: 158 countries were already recipients of U.S. military training in 2012, and about $15 billion has been spent annually in recent years on security assistance through the State and Defense departments. Nor is the strategy much in question; stronger local forces are essential to countering the proliferating affiliates of al-Qaeda. But the president’s request, which was sent to Congress at the end of last month, nevertheless raises some disturbing questions.

One is what to do when local armies are not up to the task of defeating al-Qaeda, even with U.S. training and help. That was the case in Mali, where a U.S.-trained officer led a coup against a democratic government and U.S.-supplied and -drilled army units crumbled in the face of an offensive by ethnic and Islamist insurgents. Now Iraq’s U.S.-trained forces have allowed much of the country to be overrun by al-Qaeda and Sunni tribal fighters and appear to lack the firepower to prevent the consolidation of a terrorist-ruled state.

The capture of Mali’s capital by al-Qaeda was averted only by a quick deployment of French troops in early 2013. Mr. Obama’s strategy doesn’t make clear how similar threats can be managed. If the new al-Qaeda state in Iraq and Syria cannot be defeated by local forces, will the United States allow it to remain?

A related problem concerns the behavior of foreign units that receive U.S. training and funding. If U.S.-backed forces commit human rights abuses, the damage is twofold: The fight against insurgents is compromised, and so is support for alliance with the United States.

In this image provided by NATO Training Mission - Afghanistan, a convoy of Afghan National Army HMMWVs line up in formation at the Kabul Military Training Center. (Ernesto Hernandez Fonte/AP)

Congress sought to deal with this problem in 1997 by passing the Leahy amendment, a provision named after Sen. Patrick Leahy (D-Vt.) that prohibits aid to units and individuals thought to be involved in gross human rights violations. The legislation has had a far-reaching effect: In 2011, aid was withheld from 1,766 individuals or units in 46 countries, and State Department staff vetted some 200,000 individuals and units, according to the New York Times. Senior U.S. military officials have told Congress that the restrictions helped improve major U.S. aid programs in Colombia and Afghanistan. Some countries, such as Bangladesh, have taken steps to punish offenders in order to win a restoration of aid.

Such vetting ought to be built into the new partnership program. But the administration is seeking to neuter the Leahy amendment by giving the defense secretary the authority to disregard it by asserting that “it is in the national security interest to do so.” In fact, allowing aid to flow to foreign military units that commit major human rights crimes cannot be in the U.S. interest in any circumstances. Congress should reject the ­exemption.