The Minneapolis Urban League is closing its alternative high school, coming a month after criticism from state and Minneapolis School District officials that the agency was double billing for its work helping at-risk teenagers.

The alternative high school will close June 5, ending a 40 year partnership with the Minneapolis Public Schools.

“This is a sad day for the Urban League Academy and community,” Steven Belton, interim President and CEO, said in a statement. “Our students found caring and encouraging teachers and an environment of mutual support and high expectations there.”

Belton said the Urban League will continue to advocate for educational issues and develop strategies for new educational services. He said the decision to close had nothing to do with the recent scrutiny, but is due to ongoing financial problems at the school.

Minneapolis school officials originally proposed only a one-year renewal of its contract with the school because of a lack of success in graduating the city’s most troubled high school students. That deal fell apart when the Urban League told the district it was leasing its school space to a start-up charter school, which would provide more money for the cash-strapped organization.

The Urban League has been looking for ways to increase revenue through new programs. The Star Tribune reported on one of those programs, called the 13th grade. School officials and state leaders had expressed concern that the Urban League Academy was too closely overlapping its mission and student rosters with the 13th Grade, which is state funded.

Minneapolis school officials had been giving the Urban League $800,000 a year, while the state is giving the organization $300,000 annually for the 13th Grade.

Urban League officials had said there was nothing in the two contracts that prevented double billing, and that the two programs had started to move different directions, with the 13th Grade focused more on job training and placement.

“We thank the Minneapolis Urban League for their years of service and partnership,” Minneapolis interim Superintendent Michael Goar said. “We are committed to working closely with families to provide a smooth transition for students and to meet their academic needs for this upcoming school year.”

The Urban League alternative school program focused on students who were not succeeding in the traditional public school settings. As a result of the school closing, there are 70 students who will soon be without a school.

Leslie Lewandowski, the director of Minneapolis’ Contract Alternative Schools, said those students will be placed in other alternative programs or in their community school.

“I met with the students when they were informed that the school was closing,” Lewandowski said. “The district is here to support them to make sure their transition is as smooth as possible.”

Belton said the school district money for the Urban League academy had not kept pace with costs, creating operating losses for the past several years.

The organization tried unsuccessfully to find another space for its Urban League Academy.

Belton said that contract alternative schools, like its academy, do not receive special lease aid from the state, like charter schools. These alternative schools also lose out on local tax levy revenue, dropout prevention assistance and other program money that traditional public schools are eligible to receive.

“The financial issues are complicated, but the disappointing reality is we cannot afford to provide the quality education our students deserve under the present funding structure,” said Clinton Collins, Jr., the Urban League’s board chairman. “Ultimately we decided our duty of financial stewardship necessitated closing the school.”

The Urban League will hold its final graduation ceremony for the class of 2015 at 6 p.m. on June 1.

Twelve students will be graduating from the academy.