Lowell General Hospital is planning to close a 22-year-old clinic that treats hundreds of underweight and malnourished children in one of the state’s poorest cities, saying it is losing money on the program.

The clinic, scheduled to shut down at the end of September, served nearly 450 children in the past year. Many have undiagnosed medical issues, such as allergies, reflux, or developmental delays, while others do not have enough food to eat at home or housing challenges.

Lowell General, which took over the clinic in 2012 as part of a merger with Saints Medical Center, has invested more than $600,000 in the program since then, hospital spokesman Will Courtney said. Health department funds — about $100,000 a year — cover about half of the clinic’s expenses, he said.

“For our community hospital, the program isn’t financially sustainable in the long term,’’ Courtney said in an e-mail.

Brooke Hynes, spokeswoman for the hospital’s parent company, Wellforce, said Lowell General still will provide services to underweight and malnourished children through other hospital programs and specialists. “We are committed to caring for [this] important population,’’ she said.

Hynes said the hospital would consider partnering with another organization to run the clinic.

Lowell General and its related entities lost $7.7 million on operations in 2017. Yet, Wellforce’s top executive, Normand Deschene, earned almost $3.9 million in compensation in 2016, an 83 percent increase from the prior year. Hynes said the increase was largely related to retirement benefits.

“Food insecurity’’ is very much an issue in Middlesex County, where Lowell is located, and across the state, said Allison Bovell-Ammon, deputy director of policy strategy for Children’s HealthWatch, a nonprofit research organization based in Boston. Nine percent of families in the county say they cannot afford enough food for everyone in their household.

“Even at the most mild level of food insecurity, when parents report running out of food before the end of the month, we see an impact on child health and development,’’ she said.

The Lowell clinic is part of a network of growth and nutrition clinics the state Legislature and the Department of Public Health launched beginning in 1984, when new data showed surprisingly widespread malnutrition among Massachusetts children. Those who work in the field say the need remains strong but add that state funding for the clinics has not kept up.

Boston Medical Center has the state’s largest and oldest growth clinic, begun by Dr. Deborah Frank 34 years ago. The clinics identify the causes of a child’s failure to grow and deploy a team of pediatricians, nurse practitioners, dietitians, and social workers to treat and monitor children over many months, including visiting families at home and connecting them to food sources.

Many more children in resource-rich Massachusetts are malnourished than people realize, Frank said. These youngsters are susceptible to infections because of weakened immune systems. Before the Boston Medical Center program opened, about half of malnourished children there ended up in the hospital. Now the rate is about 5 percent, Frank said.

Infections can be treated with antibiotics, but it’s harder to address long-term harm from malnutrition such as attention deficit disorder and emotional problems.

Boston Medical Center depends on philanthropy to cover about two-thirds of the $1 million annual cost to run the clinic, a satellite clinic in Brockton, and a related prevention program.

“The problem is state funding has not substantially increased in a long time,’’ Frank said. “The need is getting greater.’’

Ann Scales, a health department spokeswoman, said state money is not intended to fully fund the programs, which are expected to bill Medicaid and private insurers for some services such as doctors’ appointments. She said funding increases are planned for this year.

When Lowell General notified public health officials in the spring that the hospital was closing the clinic, the state requested proposals from other facilities. None responded. The department recently sent out a new proposal that allows programs greater flexibility in how they run the clinic. Now, Lowell Community Health Center is considering applying.

Two other hospitals, Saint Anne’s Hospital in Fall River and Baystate Medical Center in Springfield, closed their health department-funded growth and nutrition clinics in 2015.

Baystate left the program because the health department did not increase funding between 2007 and 2015, and because the hospital could not comply with the state’s performance and reporting requirements, spokesman Keith O’Connor said.

Saint Anne’s opened its own program without state funding.

Liz Kowalczyk can be reached at kowalczyk@globe.com.