Earlier this month the Obama administration announced it was cutting military aid to Egypt by hundreds of millions of dollars.

The move had nothing to do with the budget battle in D.C. Rather, it was a belated reaction to last July’s military coup against President Mohamed Morsi’s increasingly autocratic Islamist government.

Unfortunately, the administration has taken three months to come up with the wrong reaction.

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The cutback in military aid is likely to trigger an anti-American backlash in Egypt, undermine our reputation as a reliable ally and accelerate the decline of U.S. influence in the Middle East.

Ostensibly the cuts are meant to encourage a democratic evolution in Egypt. The intent is to pressure the military-backed transitional government to negotiate with Morsi’s Muslim Brotherhood and include it in future elections.

But the anti-Western Muslim Brotherhood is not a genuine democratic movement. It amply demonstrated that by ramming its Islamist agenda down the throats of Egyptians during its one year in power. Morsi’s rigid authoritarian rule provoked massive popular protests.

The army stepped in to avert a civil war and now sees itself engaged in a life and death struggle with the Brotherhood.

It knows that if it allows the Brotherhood to make a comeback, it will be targeted for purges, show trials and executions.

Given that reality and Morsi’s track record as a budding dictator, it is extremely naïve to believe that forcing the army to accept a renewed bid for power by Morsi’s Islamist supporters would help Egypt make the very difficult transition to become a stable democracy.

Instead, the likely result would be more political instability and rising violence.

President Obama should have used aid as leverage before the coup, to brush back Morsi’s aggressive and unconstitutional efforts to consolidate power. Instead, the U.S. voiced uncritical support for Morsi, alienating Egyptian liberals and secularists, as well as the army.

After the July coup, the administration announced it was suspending $585 million in U.S. military assistance to Egypt (about half of Cairo’s annual $1.3 billion allotment), pending a policy review.

After several months of handwringing, the administration has decided to withhold most of that aid, with the exception of funds slated for counter-terrorism and border security programs.

Those initiatives focus on containing Islamist extremist threats, particularly in the Sinai Peninsula near the Israeli border.

The decision tries to split the difference between the Pentagon, which argued that aid to Egypt furthers U.S. security interests, and human rights activists who contend that Egypt’s new government must be punished for its crackdown against the brotherhood. But splitting the baby is likely to satisfy nobody in Washington or Cairo.

Instead, a partial aid cutoff is likely to further erode American influence in Egypt, which has declined rapidly under President Obama. It risks rupturing ties to Egypt’s military, which shares American concerns about Islamist extremism and offers the best hope of eventually salvaging a stable democratic system in Egypt.

The New York Times reported that President Obama felt compelled to act after street clashes erupted in several Egyptian cities recently, killing more than 50 people. But the U.S. should not abandon long term allies in response to political violence provoked by the Muslim Brotherhood or other groups hostile to U.S. foreign policy. This will only encourage the brotherhood to escalate its campaign against the new government.

Moreover, publicly humiliating Egypt’s military-backed government could provoke a backlash against the U.S. and undermine Egyptian compliance with the 1979 peace treaty with Israel.

Washington would do much better to press Cairo privately to remain committed to its roadmap for restoring democracy.

Unfortunately, the administration’s decision to cut military aid to rescue the Muslim Brotherhood will only make a bad situation worse. That clearly runs against the expressed interests of most Egyptians, U.S. allies such as Israel, Jordan and Saudi Arabia, and long-term U.S. interests as well.