DIFFA, Niger — Only 2 years old, Fatouma Ouseini lay in a hospital room, undernourished and listless from fever.

She is among the nearly half a million children expected to endure the food crisis that has plagued the Lake Chad region in the past year, aid groups say, a disaster brought on by Boko Haram’s relentless campaign of killing, kidnappings and looting of entire villages.

Fatouma and her family fled from just across the border in northeastern Nigeria, the epicenter of the war with Boko Haram, where scattered areas have teetered on the brink of famine for most of this year, according to the United Nations. Now, some aid workers fear that similar conditions could spill over to bordering areas like here in Niger, putting even more children at risk.

More than 70,000 people fled their homes along the border between Niger and Nigeria in the first half of this year after militant attacks increased. Many have resettled in Diffa, living in labyrinth-like neighborhoods of mud-brick homes, competing with longtime residents for food and water.

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Children like Fatouma are so common that the town’s small hospital has dedicated an entire wing to treating malnutrition and the illnesses that stem from it.

“At home, we had everything to eat and drink,” said Hadja Mahamadou, Fatouma’s aunt, who accompanied her to the hospital. “Here, we’re waiting always for food.”

Even in normal times, northeast Nigeria and areas along the borders of Niger, Cameroon and Chad often suffer from a lack of food. It is home to some of the poorest people and highest birthrates on the planet, and their fate often lies with the quality of the year’s crop.

But farming is all the more difficult now. Some farmers have shifted to only crops that grow close to the ground so militants cannot hide in fields. Some farmers are able to sleep in encampments for safety at night, returning periodically to check on crops.

Elsewhere, the presence of militants has prevented farmers from going to their fields. In some areas, farmers have missed the last three harvest seasons.

Boko Haram has routinely stolen herds of cattle and raided markets to feed its ranks. Fighters sometimes even send suicide bombers to blow up shoppers, killing scores of civilians. On Friday, two young girl suicide bombers killed nearly 60 people and wounded dozens more in two attacks on markets in rural northeastern Nigeria.

In response, the military in many areas has shut down markets, cutting off supplies for militants but also for citizens, compounding a food crisis already in full swing.

Nigeria has been particularly hard hit. It continues to writhe from a drop in oil prices that set off a currency devaluation and now a recession. Food prices have soared even in major cities far from areas where Boko Haram operates. High prices have rippled into neighboring countries that rely on Nigeria for trade.

Some aid workers complain that Nigeria’s government, which prides itself on being one of Africa’s biggest economies, had been reluctant to accept help from food delivery groups until this summer. This fall, a Nigerian Senate report said $8 million in aid meant for the northeast had been misallocated or had disappeared.

President Muhammadu Buhari, who pledged during his campaign to rid the country of Boko Haram after years of torment, has declared the militants defeated despite their continued attacks.

This month, the United Nations announced that it needed about three times as much money as it originally expected to mitigate the food crisis and other problems in the region, which are likely to continue in Nigeria at least until the harvest season at the end of 2017. The organization, which has struggled to raise money to help the region, is now asking for $1 billion for northeastern Nigeria.

“We have underestimated the scale and complexity of the crisis in northern Nigeria,” said Peter Lundberg, the United Nations’ deputy humanitarian coordinator in Nigeria.

Mr. Buhari immediately dismissed the appeal, insisting that the world organization was exaggerating the humanitarian crisis in his country to increase donations. In a statement signed by his spokesman, Mr. Buhari said the United Nations was engaging in “a type of hype that does not provide a solution to the situation on the ground but more to do with calculations for operations financing locally and abroad.”

Later, the government’s official Twitter account posted that it recognized the severity of the humanitarian situation.

While crediting the United Nations with immeasurable help to assuage the food situation, Mr. Buhari said, “The hype, especially that which suggests that the government is doing nothing is, therefore, uncharitable and unnecessary,” according to the statement.

“We are concerned about the blatant attempts to whip up a nonexistent fear of mass starvation by some aid agencies, a type of hype that does not provide a solution to the situation on the ground but more to do with calculations for operations financing locally and abroad,” the statement said.

Col. Adamu Laka of the Nigerian military said some areas of Nigeria — like Bama, a city where humanitarian groups had described severe malnourishment after it was liberated from Boko Haram control in June — were so flush with food that the military had told the authorities to slow shipments. But he said few farmers in the area had cultivated their own fields and instead were relying on relief food.

“Right now, there is no problem of food in Bama,” he said. But if the relief stops, “that is when there will be a problem.”

In Nigeria, the threat of militants has blocked access for aid groups like the United Nations’ World Food Program to some villages until midyear. The organization initially handed out cash and vouchers for food, a system that officials now acknowledge was a mistake in an area where inflation had set in. Now, the United Nations is directly distributing rice and other food.

But encampments of displaced people, even in the accessible and relatively safe Nigerian city of Maiduguri, with its huge markets, still lack enough food and water. A United Nations assessment showed that one informal camp called Muna Garage, home to 17,000 people who have fled militants, is in dire need of water wells and food.

“No one here is dying of starvation, but with chronic malnutrition, when they get malaria or any other communicable disease, they die from it,” said Mr. Lundberg, who acknowledged past gaps in the agency’s handling of the food crisis.

Poor coordination and major turnover in leadership have dogged agencies of the United Nations, criticisms that were pointed out in a stinging letter sent last month to the organization’s emergency directors by officials at the European Union.

“Recent reports indicate that even where access is relatively good, like in parts of Maiduguri, scaled-up delivery has been inadequate and emergency conditions prevail for the local population,” the letter said.

Mr. Lundberg conceded the criticisms but said they were outdated. The organization recently set up offices in northeast Nigeria, brought in experts who dealt with famine in South Sudan and is working “in a completely different way to address the gaps that clearly were there.”

Here in Niger, humanitarian workers say food deliveries are flowing. At one encampment outside Diffa on a blazing recent afternoon, hundreds of people gathered alongside a truck for handouts from the International Rescue Committee with pink bags of Happy Family brand rice, macaroni, palm oil, bouillon and other food.

Fati Fougou, 40, who has been running from Boko Haram for two years, had been waiting for the shipment since she returned from morning prayers. She said each ration was supposed to be a month’s worth of food for one family. But hers, intended to feed her and her seven children, generally runs out after 25 days.

“It’s not sufficient,” Ms. Fougou said. “But it’s good to have.”