One year after the revolution that ousted President Hosni Mubarak, the Egyptian military is closing down civil society organizations and trying to manipulate the constitution-writing process to serve its narrow interests. Meanwhile, in Pakistan, where the military has also held sway for more than half the country’s existence — for much of that time, with America’s blessing — a new civil-military crisis is brewing.

For the United States, the parallels are clear and painful. Egypt and Pakistan are populous Muslim-majority nations in conflict-ridden regions, and both have long been allies and recipients of extensive military and economic aid.

Historically, American aid tapers off in Pakistan whenever civilians come to power. And in Egypt, Presidents George W. Bush and Barack Obama both resisted pressure from Congress to cut aid to Mr. Mubarak despite his repression of peaceful dissidents.

It is no wonder that both Egyptians and Pakistanis express more anger than appreciation toward the United States. They have seen Washington turn a blind eye to human-rights abuses and antidemocratic practices because of a desire to pursue regional objectives — Israeli security in the case of Egypt, and fighting Al Qaeda in the case of Pakistan.

The question now is whether the United States will, a year after the Egyptian revolution, stand by and allow the Pakistani model of military dominance and a hobbled civilian government to be replicated on the Nile.

Pakistan and Egypt each have powerful intelligence and internal security agencies that have acquired extra-legal powers they will not relinquish easily. Pakistan’s history of fomenting insurgencies in neighboring countries has caused serious problems for the United States. And Egypt’s internal security forces have been accused of involvement in domestic terrorist attacks and sectarian violence. (However, Washington has long seen Egypt’s military as a stabilizing force that keeps the peace with Israel.)

The danger is that in the future, without accountability to elected civilian authorities, the Egyptian military and security services will seek to increase their power by manipulating Islamic extremist organizations in volatile and strategically sensitive areas like the Sinai Peninsula.

Despite the security forces’ constant meddling in politics, Pakistan at least has a Constitution that establishes civilian supremacy over the military. Alarmingly, Egypt’s army is seeking even greater influence than what Pakistan’s top brass now enjoys: an explicit political role, and freedom from civilian oversight enshrined in law.

Egypt’s army was once considered heroic for siding with peaceful demonstrators against Mr. Mubarak, but it has badly mishandled the country in the past year. The riot at a soccer match on Wednesday that killed around 70 people underscored the leadership’s failure to undertake badly needed police reform and restore security. The economy is teetering, peaceful demonstrators have been tried in military courts, anti-Christian violence has spiked and ministers appointed by the military have hounded civil society groups that advocate government accountability, budget transparency, human rights and free elections.

A dismayed Congress has attached conditions to future military assistance to Egypt (now $1.3 billion a year), requiring the Obama administration to certify that the military government is maintaining peace with Israel, allowing a transition to civilian rule and protecting basic freedoms — or to waive the conditions on national security grounds — if it wants to keep aid flowing.

The Egyptian military is clearly not meeting at least two of those three conditions right now. Consequently, the Obama administration should not certify compliance, nor should it invoke the national security waiver by arguing that Egyptian-Israeli peace is paramount and that Egypt’s military is the only bulwark against Islamist domination of the country — because both of these arguments are deeply flawed.

First, hardly anyone in Egypt favors war with Israel, and a freeze or suspension of American aid would not change that. Second, continuing support to an Egyptian military that is bent on hobbling a liberal civil society would only strengthen Islamist domination. Islamist groups won some 70 percent of seats in the recent parliamentary elections, but they will now face tremendous pressure to solve the deep economic and political problems that caused the revolution.

In Egypt, as in Pakistan, the ultimate solution is a peaceful transfer of power to elected, accountable civilians and the removal of the military’s overt and covert influence from the political scene. At a minimum, Egypt should establish the clear supremacy of the civilian government over the military and allow an unfettered civil society to flourish.

Washington should suspend military assistance to Egypt until those conditions are met. Taking that difficult step now could help Egypt avoid decades of the violence, terrorism and cloak-and-dagger politics that continue to plague Pakistan.

Michele Dunne, a former White House and State Department official, and Shuja Nawaz, the author of “Crossed Swords: Pakistan, Its Army, and the Wars Within,” are the directors of the Middle East and South Asia centers, respectively, at the Atlantic Council. This article was originally published in The New York Times. Photo credit: Getty Images.