WASHINGTON — The Education Department has ordered Duke University and the University of North Carolina at Chapel Hill to remake the Middle East studies program run jointly by the two schools after concluding that it was offering students a biased curriculum that, among other complaints, did not present enough “positive” imagery of Judaism and Christianity in the region.

In a rare instance of federal intervention in college course content, the department asserted that the universities’ Middle East program violated the standards of a federal program that awards funding to international studies and foreign language programs. The inquiry was part of a far-reaching investigation into the program by the department, which under Betsy DeVos, the education secretary, has become increasingly aggressive in going after perceived anti-Israel bias in higher education.

That focus appears to reflect the views of an agency leadership that includes a civil rights chief, Kenneth L. Marcus, who has made a career of pro-Israel advocacy and has waged a yearslong campaign to delegitimize and defund Middle East studies programs that he has criticized as rife with anti-Israel bias.

In this case, the department homed in on what officials saw as a program that focused on the region’s Muslim population at the expense of its religious minorities. In the North Carolina program’s outreach to elementary and secondary school students, the department said, there was “a considerable emphasis placed on the understanding the positive aspects of Islam, while there is an absolute absence of any similar focus on the positive aspects of Christianity, Judaism or any other religion or belief system in the Middle East.”