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Last month at West Point, President Obama pledged support for democracy-promotion programs. "For unlike other nations, America is not afraid of individual empowerment," he said. "We are strengthened by it. We're strengthened by civil society. We're strengthened by a free press."

Given that commitment, it's perplexing that the White House, in the appendix to next year's budget, has proposed to undo the so-called Brownback amendment. This provision bars any administration from asking for foreign regimes' approval before sending democracy-promotion aid. Passed in 2005 at the urging of Republican Sam Brownback, then a senator and now the governor of Kansas, the amendment ensured that non-governmental organizations disfavored by repressive regimes would be supported by the United States instead of being subject to unfair registration processes.

To change the policy would be to send an unfortunate message: If democracy-promotion programs have to be compromised to protect strategic alliances, so be it.

The budget proposal is stoking fear among such NGOs. The Project on Middle East Democracy, which issued a report this month on Mr. Obama's 2015 budget, said the proposal "confirms widespread suspicion that the administration has essentially lost interest in fighting to protect such [human] rights."

The administration's record has already fueled such suspicion. In 2012, Egyptian security forces raided foreign NGOs, charging 19 Americans and two dozen other activists. The Obama administration did little, and the Egyptian government remained one of the top recipients of U.S. assistance. This year, despite the U.S. Agency for International Development's commendable new strategy on democracy and human rights, Mr. Obama's proposed funding to Arab democracy programs is lower than in 2010.

Asked about the proposal, the State Department responded, "The administration's requests frequently recommend that Congress remove restrictions and requirements that constrain flexibility to manage foreign policy, are overly burdensome, and/or are unnecessary due to policy or procedures already in place."

In fact, the lack of flexibility here should be welcomed. With this restriction, the Obama administration can tell regimes that Congress has tied its hands on democracy-promotion programs. The removal of the amendment would make U.S. support for these programs negotiable, thereby risking their viability.

These programs are crucial for the United States in the long term. As Mr. Obama said of Egypt and Burma in the same West Point speech, "In each of these cases, we should not expect change to happen overnight. That's why we form alliances — not only with governments but also with ordinary people."

Eliminating the Brownback amendment would undermine those crucial alliances with ordinary people.