Southeast Asia is a key front in the global war against Islamist terrorism, and the region has seen some notable counterterror successes. The Philippines, however, is in danger of taking a big step backward. Witness the unprecedented autonomy agreement President Gloria Macapagal Arroyo is trying to strike with the Moro Islamic Liberation Front, or MILF, the largest armed Islamist separatist group in Southeast Asia.

[Gloria Macapagal Arroyo]

Called the Memorandum of Agreement on Ancestral Domain, the deal would grant Muslims significant governing autonomy and the right to live under Shariah law in an expanded area of the archipelago's southern islands. The deal is designed to appease Muslims who want to break away from the Philippine nation and unify with other Muslims in the region. Under the agreement, 700 towns, many with sizable Christian populations, would be turned over to Islamic rule. Residents and local leaders were not consulted about the transition, and a constitutional amendment would be necessary to free Muslim areas from national governance. Such a national campaign to empower Muslims faces an uphill battle in a country whose population is 93% Christian. Which is just as well, since it would be a major mistake for at least four reasons:

First, by carving up provinces into separate Muslim and Christian enclaves, the deal would surrender any hope that Filipinos can find a way to live together and instead falls back on the myth that countrymen can live healthy "separate but equal" lives in an apartheid-like arrangement. This would undo the decade of progress toward greater political integration since former House Speaker Jose de Venecia started welcoming Muslim representatives into his ruling congressional coalition.

Second, it would increase rather than decrease the likelihood of territorial disputes because the agreement concedes to claims that the region constitutes a traditional Islamic homeland. This would likely inflame Christians, who would be kicked off of land where they have lived for decades when Muslims make claim to their legally mandated "ancestral domain."

Third, further removing Muslims from the rest of Philippine society and enabling them to shape an entirely separate culture would encourage the separatist mentality that dreams of carving out a pan-Islamic state from other existing countries in the region, such as Malaysia, Indonesia and Singapore. This has been a MILF goal since its founders broke off from the Moro National Liberation Front in the 1980s after that group made peace with Manila.

Lastly, and perhaps most importantly for the outside world, greater Islamic independence and less Philippine control over the Islamic regions would invite even more terrorist activity in an area that already has strong ties to al Qaeda. With the deployment of U.S. Special Forces to the southern Philippines now in its seventh year, joint U.S.-Philippine operations have pacified the most lawless Muslim areas. Expanding the Islamist sphere of influence now threatens to undo this success.

The Arroyo administration's openness to relinquishing control of so much territory has stirred up massive protests. On Monday, the Philippine Supreme Court temporarily put the brakes on the deal, which was scheduled to be signed in Kuala Lumpur on Tuesday. Without a doubt, Manila needs to significantly reform the way it deals with its Muslim minority, which has long been neglected, particularly in the government appropriations process. However, a more worthwhile policy would be to improve the lives of isolated Muslims so that they could be assimilated into greater society, not further excluded from it.

Then again, this agreement may not even be about the Muslim areas at all. The most plausible explanation for Ms. Arroyo's support for such a problematic deal is that it's a ploy to consolidate her own hold on power.

Expanding Muslim autonomy would require changes to the Constitution, which would in turn require a constitutional convention. The likelihood this deal would pass such a convention is virtually nil. But Philippine law does not allow for limits to be placed on the mandate of a constitutional convention, or, for that matter, for the agenda to be predetermined. This means that once the convention was called, the door would be open to discussing other constitutional changes -- like the switch from a U.S.-style presidential system with a bicameral legislature to a unicameral system run by a prime minister.

That just happens to be a pet project of Ms. Arroyo's, not least because it would pave the way for her to stay in office past the end of her current constitutionally term-limited single term, which expires in 2010. Reformists have previously expressed their willingness to put Ms. Arroyo in the ceremonial role of President Head of State that supporters of the parliamentary system envision creating. But the reformers wouldn't have enough support to call a constitutional convention explicitly to enact this reform. So rather than a half-baked attempt at brokering peace with Philippine Muslims, President Arroyo's support for greater Islamic autonomy can thus be seen as a Trojan Horse to extend her stay in Malacanang Presidential Palace by forcing a constitutional convention to be called on a separate issue.

That's crazy, and the scheme may well not succeed. But Ms. Arroyo has shown herself to be a deft politician in the past. The real problem, though, is that this entire episode suggests she's more interested in playing domestic politics than she is in fighting the war on terror. Countries in Asia that have racked up the biggest counterterror successes -- like Indonesia -- have done so because political leaders have been willing to stand up to strong political interests and focus on counterterror policing. Ms. Arroyo isn't showing that kind of resolve, and the consequences both for the Philippines and its neighbors could be serious.

Mr. Decker, a former editorial page writer for The Wall Street Journal Asia, is an adjunct professor of government at Johns Hopkins University.

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