S. Allen Counter, associate professor of Neuroscience at the Medical School, will become the first director of the Harvard Foundation, a new organization for promoting racial understanding at the University.

Counter will begin supervising the controversial campus organization--which was proposed in January by a nine-member student-faculty committee--at the beginning of the school year.

Formerly a full-time associate professor of Biology. Counter has been named to a half-time Med School associate professorship and the half-time Foundation directorship.

Counter was in New York City at the Rockefeller University yesterday and could not be reached for comment. President Bok said yesterday the most important tasks before Counter now are "putting together a strong and interested group of Faculty members for the Foundation councils, and...figuring out how students will be involved."

Counter will also have to "assert considerable imagination and ingenuity on activities that could be proposed in order to give it (the Foundation) concreteness." Bok said.

Rev. Peter J. Gomes, Plummer Professor of Christian Morals and the chairman of the committee that proposed the Foundation, said yesterday he was "delighted" with Counter's appointment.

"He's got to look to establish some kind of credibility with the Faculty." Gomes said, adding. "And he's got to perform the very delicate balancing act of making the Foundation popular with the general student community as well."

The Gomes Committee recommended the Foundation consist of three parts:

* a student committee of representatives of various minority organizations as well as majority students:

* a 12-member committee of Harvard faculty and staff:

* a group of about ten "associates" from around the country who will advise the Foundation and help raise funds for its program.

In March, the student Third World Center Organization, which presented the first proposal for an institution to serve primarily minorities in the spring of 1980, withdrew its support of the Gomes Committee's proposal, saying it would stress race relations, not minority needs.

Black student leaders could not be reached for comment yesterday.

While Faculty approval of the Committee was not required for establishment of the Foundation, the Faculty debated the proposal in March and gave it generally lukewarm support.

At the Faculty meeting. Nathan I. Huggins, chairman of the Afro-American Studies Department, said the University could best improve race relations through existing institutions, such as the Houses, rather than through a Foundation.