President Obama pauses as he listens to a question during a town-hall meeting at Benedict College on Friday in Columbia, S.C., about the importance of community involvement. (Carolyn Kaster/AP)

The country’s first African American president is finding himself increasingly at odds with a cornerstone of the African American community: historically black colleges and universities.

Leaders at these schools and some black lawmakers say the Obama administration has been pushing policies for years that hurt students at a time when historically black colleges are already cash-strapped and seeing a drop in enrollment.

Tensions spilled over after a recent Congressional Black Caucus meeting with Obama and Vice President Biden in which the president said that historically black schools, also known as HBCUs, needed to do a better job graduating students and not saddling them with debt, according to several people at the meeting. Some Black Caucus members bristled at those remarks since they say the president didn’t acknowledge that his own administration was also pursuing policies that advocates say are hurting the schools.

“The president thinks that HBCUs — and there may in fact be some — are failing our students,” said Rep. Marcia L. Fudge (D-Ohio), who was in attendance. “But there needs to be an open dialogue about higher education and why HBCUs have historically gotten short shrift when it comes to resources and recognition.”

On Friday, President Obama visited Benedict College, a historically black, liberal arts college in Columbia, S.C., as part of a push for his initiative called “My Brother’s Keeper” aimed at helping young black men.

But he did not mention historically black schools that have been hailed for their work educating young African Americans. Many of the schools are strapped for cash after years of financial mismanagement, poor alumni giving and fluctuating levels of government support. They are seeing a drop in enrollment, and many are struggling to graduate students on time.

Critics of the administration say that rather than help these schools at a time of acute need, the president keeps ignoring them or enacting policies that hurt them.

At last month’s meeting of the White House’s advisory board on historically black colleges and universities, the board’s chairman delivered some blunt criticism to the administration.

“We are not consulted when it comes to policy changes and decisions impacting — in a major way — the institutions on whose behalf we are to advocate,” Hampton University President William Harvey, who chairs the advisory board, said at a board meeting in February. “Overall support to black colleges is down.”

HBCU advocates also point to a restrictive federal loan policy that they say has shut out many families interested in sending their children to historically black colleges. The administration is also getting ready to unveil a new college ratings system that HBCU leaders say could unfairly keep their schools from getting more aid. And when the president recently unveiled a new initiative to pay for community college tuition, he did it without consulting HBCU leaders, who say their schools should also be eligible for help since they also serve low-income students.

The White House declined to comment on the meeting with Black Caucus members. But not everyone at the meeting took offense to Obama’s comments on the performance of historically black schools. “It wasn’t a dig at HBCUs,” said Rep. Danny Davis (D-IL). “We need to direct as much assistance to these schools because what they’re doing is invaluable.”

The Education Department points out that revenue to HBCUs from the federal government decreased during the recession, prior to Obama taking office, and increased across the board during the first two years of his administration. Federal funding of the schools from the Department of Education has increased 40 percent since 2007, including grants for more African American students.

“The administration is strongly supportive of historically black colleges and universities,” said Education Undersecretary Ted Mitchell. “We have been strong supporters in word and deed.”

The nation’s 105 historically black schools, including Howard University and Morehouse College, account for just 3 percent of student enrollment at two- and four-year colleges. Yet they enroll 9 percent of black undergraduates and award nearly 20 percent of the bachelor’s degrees earned by African Americans, according to the National Center for Education Statistics (NCES).

Obama started off his presidency on a high note with historically black schools. His stimulus package earmarked millions of dollars for infrastructure projects, academic research and overall operations at black colleges. But budget fights, across-the-board cuts in federal spending and changes in education policy reversed many of those gains.

Supporters of the schools say they have been hit particularly hard by a 2011 decision from the Education Department to tighten lending standards to parents for federal loans covering their children’s tuition. Federal parent loans have a 7.9 percent interest rate, compared with 3.4 percent to 6.9 percent for student loans.

The United Negro College Fund estimates that about 28,000 students at black colleges dropped out during the 2012-13 academic year because their families could not get loans.

After two years of discussions with black lawmakers and educators, the department relaxed the lending criteria. Starting in July, it will only check the past two years of parent credit histories, down from the five originally proposed.

But HBCU administrators say the damage was already done, costing black schools more than $150 million in revenue.

Another source of contention between the administration and HBCUs is a new college ratings system being fleshed out by the Education Department that would grade schools on their access, affordability, completion rates and graduate employment, among other things. By 2018, schools with high ratings could be eligible for larger Pell Grants and lower rates on student loans.

Many higher-education experts worry that the system will favor selective schools with deep pockets that serve students with means. That could deal a blow to historically black schools that enroll students who are not academically or financially prepared, said David Wilson, president of Morgan State University.

“I just don’t see how you can have a system that is going to be fair . . . especially when you have one set of schools doing the heavy lifting and another set fishing in a different pond,” he said.

About 72 percent of students at historically black schools are eligible for Pell Grants, a form of federal aid that goes to the neediest applicants, and nearly as many take out federal loans. Many are the first in their family to go to college and often have to work and take courses.

Education Secretary Arne Duncan told the president’s advisory board on HBCUs that the ratings “will take account of the degree of difficulty that many institutions, including ­HBCUs, face in educating significant numbers of underprepared, disadvantaged students.”

“I understand why HBCUs would be apprehensive,” said Ivory Toldson, deputy director of the White House initiative on HBCUs. “But what the administration is saying is we need a system that rewards the success of institutions that take greater risk with students, that do a better job with lower-income students.”

Advocates of historically black schools were disappointed again when Obama presented an ambitious new plan to cover tuition at the country’s community colleges — and many say they were not consulted before the policy was presented.

Facing flagging enrollment and strained finances, some black college leaders view Obama’s proposal for two years of free community college as a threat.

“If you’ve got $60 billion to spend over the next 10 years, send it to Pell [Grants],” said Michael L. Lomax, president and chief executive of the UNCF, referring to the projected cost of Obama’s community college initiative.

He said he is also disappointed that the president would steer minority students to community colleges that often have lower graduation rates than historically black schools.

Still, as student debt has surpassed the $1 trillion mark, Morgan State’s Wilson said Obama is right to demand better results from higher education.

“He really wants to see a more streamlined system, one that is more accountable,” Wilson said. “Perhaps if some conversations had taken place with institutions serving a large swath of first-generation, low-income students, some of the unintended consequences could have been avoided.”