Myanmar’s badly conceived agricultural policies are compounding the country’s already dire food situation.

In recent years, Myanmar’s reclusive military rulers have plowed large tracts of rice- and vegetable-growing land to plant jatropha — an inedible plant used for making biodiesel.  Soldiers in the country’s 400,000-strong army are routinely instructed to be self-sufficient and do so by simply seizing food from farmers.

And villagers in the highland regions are often given rice strains requiring expensive fertilizers which they can’t afford, according to academic researchers and nongovernment organizations.

Now, the folly of such policies is becoming apparent in the wake of the cyclone that devastated the country last weekend.

Much of the Irrawaddy River delta, the country’s rice bowl, is still under water and up to a million people are waiting for emergency aid to arrive from the rest of the world. At least 22,000 people have died in the storm and another 41,000 are missing, according to the military government. And U.S. officials contend the death toll may reach 100,000 people.

United Nations World Food Program official say the storm wiped out much of Myanmar’s mid-year rice harvest and add that grain stockpiles are dwindling because of the military’s jatropha drive. That makes it likely Myanmar’s plans to export rice to other needy nations such as Bangladesh this year will be scrapped.

Indeed, He Changchui, Asia-Pacific chief of the UN’s Food and Agriculture Organization said Thursday that the widespread flooding will exacerbate an already precarious domestic food supply situation. “Time is running out to prepare for the main rice-planting season,” he said.

The result: Myanmar, a major exporter before the military came to power in a 1962 coup, will probably have to start importing rice at a time when global prices for the grain have soared.

The military regime’s opaque decision-making and often bizarre policies could jeopardize prospects for Myanmar’s longer-term recovery, analysts and diplomats suggest. In particular, the regime’s mismanagement of agriculture has badly eroded the country’s food-security cushion — despite the government claims before the cyclone struck that Myanmar would produce enough rice this year to double its exports.

“We can’t blame Burma for being hit by a cyclone, but we can point to their policies for making a longer-term recovery much harder,” said a senior western diplomat in Yangon.

For example, the military regime used to require that all rice farmers give a portion of their harvest to the army. That policy was formally abolished in 2003, but it survives in practice thanks to a government directive that army battalions should strive to be self-sufficient — effectively giving soldiers a license to loot, critics say. Myanmar has also been bringing in strains of hybrid rice from China, but has failed to provide the additional fertilizer those strains need to flourish.

The most notorious example of errant policy-making, however, reflects junta leader Senior-General Than Shwe’s fascination with biodiesel to break the country’s dependence on expensive imported oil.

In December 2005, the battle-hardened, 75-year-old commander kicked off a nationwide campaign to grow jatropha, a squat, hardy bush which yields golf-ball-sized fruit containing a sticky, yellow liquid that can be made into fuel. His drive was similar to initiatives in other parts of the world, including the U.S., which encouraged farmers to grow corn, palm oil or other crops for biofuel and which are now facing intense criticism for driving up the price of food.

India, China and other countries grow jatropha on scrubby land where food crops can’t survive. But in Myanmar, some of the country’s most fertile land has been converted to cultivating the shrub, including several plantations of as much as 2,500 acres each, researchers say.

“This was the whitest of the junta’s white elephants,” said Monique Skidmore, a professor at the Australian National University and an author of two books on Myanmar. “People were being forced to grow it everywhere — in fields, in schools, along the sides of the road. It goes to show how (the generals) have no concept of how to properly run the country, especially in the aftermath of this cyclone.”

It’s not clear how much of Myanmar’s arable land has been converted to jatropha cultivation.  Organizations such as the United Nations Food and Agriculture Organization warned the government about the risks of farming jatropha on land which could be used to grow food. But Gen. Than Shwe’s goal was to set aside an area the size of Belgium to grow jatropha — a huge commitment for Myanmar, which is roughly the size of France.

In 2006, the chief research officer at state-run Myanmar Oil and Gas Enterprise said Myanmar hoped to totally replace the country’s oil imports of 40,000 barrels a day with home-brewed jatropha-derived biofuel. Other government officials declared Myanmar would soon start exporting jatropha oil.

Meanwhile, ordinary citizens were press-ganged into working in the jatropha program, according to Myanmar refugees and political activists.  State-run television showed documentaries on how to grow the plant, while headlines in state newspapers such as The New Light of Myanmar urged people to plant more jatropha shrubs.

An extensive report released earlier this month by the Ethnic Community Development Forum, an alliance of seven non-government community development organizations mostly based in neighboring Thailand, catalogs instances where the military seized private farm-land to grow jatropha or ordered farmers to switch from cultivating rice, wheat or other crops to growing jatropha instead.

In 2006, each of Myanmar’s 14 administrative zones was instructed to plant 500,000 acres of jatropha — without regard to each region’s size or its suitability for such cropping. In some places, such as the region that includes the country’s largest city, Yangon, that means around 20% of the land is supposed to be planted with jatropha, according to the forum’s report.

Despite the military’s extensive efforts, the jatropha campaign apparently has largely flopped in reaching its goal of making Myanmar self-sufficient in fuel.

In many places, the farmers didn’t understand what it was they were supposed to be farming, and the crops failed. Other people, the forum’s report said, “have been fined, beaten, and arrested for not participating.”

What’s more, jatropha turned out to be harder to refine into biofuel than Gen. Than Shwe and the junta had expected. Faced with a shortfall of fuel, Myanmar began stepping up its conventional oil imports last year just as global crude prices began to spike.

That lead to rising food and transport costs and, ultimately, contributed to a pro-democracy revolt led by Buddhist monks, which the military brutally crushed last September, killing at least 31 people.

Agricultural and aid experts worry that Myanmar’s experiment in fuel self-sufficiency has already compromised its ability to feed itself.

“I mean, they were tearing up rice paddies to plant jatropha,” said David Mathieson, a Thailand based coordinator with Human Rights Watch, who has interviewed dozens of refugees who have crossed over the border in the months before the cyclone to escape the mismanagement of Myanmar’s agricultural economy. “The farmers don’t know what they are supposed to be doing and this is going to cause a lot of trouble later on.”

Write to James Hookway at james.hookway@awsj.com