The House rejected 67-53 the additional funding after Appropriations Chairman Herb Frierson, R-Poplarville, said the $6 million would have to be taken from the five other public universities.
"You have to ask yourself are you hurting the students of the other universities?" he said.
The debate came as the House and Senate leadership are passing separate budgets in anticipation of going to conference later this month to hammer out a final budget agreement.
In 2002, the state reached a federal court-approved settlement to provide an additional $500 million over 17 years to the three historically black universities to make up for past inequities.
Alcorn State, Jackson State and Mississippi Valley State universities were charged with using the funds to enact new programs, such as an engineering school at Jackson State, and to attract other-race students. Two years ago, as part of the settlement, the level of Ayers funding was scheduled to start a stair-stepped reduction.
The funds were not reduced during the 2011 session, and the budget proposal passed by the Senate this year does not reduce the funds.
A group of black House members tried to amend the House budget to include the $6 million that is in the Senate plan. But Frierson argued that the House budget provides funds to pay the increased costs of the state retirement system, and the Senate proposal does not. That increase is scheduled to be about $48 million for all state agencies, including education.
He said if the Legislature does not provide additional funds to pay for the increase then the agencies will in effect suffer a $48 million cut this year.
Despite Ayers funding, Rep. Willie Perkins, D-Greenwood, said the three black schools still are far behind the other schools and face the risk of programs being eliminated if they do not receive additional help.
A private endowment for the three back schools that was supposed to be created with the help of Institutions of Higher Learning officials has not been funded, Perkins pointed out.
"If that had been done, we might not now be here asking for $6 million," he said.
The final decision on whether the schools will get the funds will be made in House-Senate conference.