The Education Department said Thursday it will continue funding a Middle East studies program that it accused of advancing an ideological agenda. But in the face of critics, the agency sent a warning that it would not back off its oversight of similar programs.

In August, the department ordered the Duke-UNC Consortium for Middle East Studies to revise its offerings or risk losing a $235,000 federal grant. It accused the program of promoting a positive view of Islam while virtually ignoring Judaism, Christianity and other religions.

Conservatives have long accused universities of harboring anti-Semitic bias and have called for investigations into course offerings. The agency’s August letter was seen as a move to put other universities on notice that such alleged bias would not be tolerated.

Critics in higher education accused the administration of politicizing colleges and universities and violating academic freedom. Among them was the Middle Eastern Studies Association, which charged that the Education Department’s inquiry constituted “an unprecedented and counterproductive intervention into academic curricula and programming that threatens the integrity and autonomy of our country’s institutions of higher learning.”

In a formal response to the Education Department, the University of North Carolina defended the program. It did not offer to change its programs but said it would enhance oversight of the consortium and better record how spending matches the law’s requirements.

The Duke-UNC Consortium was founded in 2005 and seeks to bring people on both campuses together for scholarly and cultural events related to the Middle East and Muslim communities around the world.

On Thursday, Education Department spokeswoman Angela Morabito said the agency had released the grant funding for the Duke-UNC program. She also released a letter sent to the Middle Eastern Studies Association defending the Education Department’s investigation. In it, Robert King, an assistant secretary at the department, wrote that the government has an obligation to make sure grant recipients are adhering to requirements set out by law.

King said the law requires programs to include “balanced perspectives.” He said the department will not, as a general rule, dictate the content of courses and programs but will insist that the legal requirement for diverse perspectives be met.

“We are simply encouraging the Consortium to offer more perspectives, not fewer, in accordance with the law,” he wrote. He said the agency had no objection to a focus on Islam but wanted expanded offerings to include other religions.

He also made clear that the department is not going to relent on similar oversight.

“Federal grants are not blank checks from public coffers, and the Department intends to ensure that taxpayer funds are spent in alignment with Congressional directives,” he wrote.