The District terminated a nonprofit’s $3 million contract to manage a new shelter for homeless families just four months after it opened, after city officials were unable to verify the backgrounds of staffers.

Officials with the D.C. Department of Human Services said Tuesday that Life Deeds Inc. would stop operating the 35-unit shelter in Ward 7, effective April 11. Life Deeds, which is based in the District, also lost a separate $852,000 contract to manage the cases of 24 families living in subsidized housing.

Contractors working with vulnerable people in the District must pass a variety of background checks, including criminal history, drug screenings and tests for tuberculosis.

City officials last month said they were unable to verify documentation about staffers that had been provided by Life Deeds. Allieu Kamara, the company’s president, said a vendor had falsified the documents.

Laura Zeilinger, director of the Department of Human Services, said that she does not believe the Life Deeds staffers posed a danger to residents and that they have been returning to the shelter after passing their clearances. She said it’s likely that a new contractor would rehire many of the same staff.

“To be clear, this is not a problem with staff and the way they were treating families or administering services,” Zeilinger said in a phone interview. “It’s important that [documentation] is valid so we can ensure that staff are appropriate to work with families and children. There was nothing that any staff member did working on the project that was an issue, but we need to work with a partner organization we can trust.”

The shelter, called the Horizon, is one of three that opened last fall as part of Mayor Muriel E. Bowser’s ambitious plan to replace the megashelter at the shuttered D.C. General campus with a network of new, smaller shelters spread across the city.

The issue of shelter staffing is particularly sensitive because police believe a janitor at D.C. General was responsible for the disappearance of 8-year-old Relisha Rudd in 2014. Bowser, a Democrat, has said repeatedly that the Rudd case drove her to close D.C. General.

Bowser, who started her second four-year term this year, often has described the closure of D.C. General as one of her proudest achievements. She has celebrated the opening of new facilities in Wards 4, 7 and 8 with ribbon-cutting ceremonies.

But problems with the Life Deeds contract, which were first reported by the Washington City Paper, surfaced in January. After they could not confirm the documentation provided by Life Deeds, city officials deployed their own workers to staff the shelter.

The contractor responded to questions about the background checks Feb. 8, but Zeilinger said the city found the response lacking and notified Life Deeds on Monday that it was nullifying the contract.

Kamara said he plans to appeal but did not specify how. He said Life Deeds is no longer working with the human resources vendor that he blamed for mishandling clearances and defended his company’s management of the shelter.

“Clients have received employment services, credit recovery, and other housing stabilization services to aid in the prevention of the return to homelessness,” Kamara said in an email. “Life Deeds has diligently worked to assist in the eradication of homelessness in the District.”

The 24 families in permanent city housing who relied on Life Deeds for case management already have been transitioned to other nonprofits, Zeilinger said.

Life Deeds holds other city contracts to provide social services, including support for people using temporary housing vouchers and group homes for troubled youth.

As of Monday, the D.C. government is housing 584 homeless families, with 118 of them living in short-term homeless shelters and most of the rest in motels.

City officials expect 121 new units for homeless families to become available this year if new shelters in Wards 5 and 6 and an additional temporary site in Ward 8 open as scheduled by the end of 2019. Construction of the remaining family shelters in Wards 1 and 3 is projected to end by 2020.