U.N. Ambassador Jeane J. Kirkpatrick said yesterday that she will refuse honors from Barnard and Smith colleges, where students and faculty members have protested her support of Reagan administration policies in Central America.

Kirkpatrick, who has been heckled this year on several campuses, announced her decision "after serious reflection," she said, in four similar and tersely worded letters to officials at the two women's colleges.

"Doubtless, we will all want to reflect on the events surrounding this episode and what they tell us about who we are and what we have become," Kirkpatrick wrote both schools.

Kirkpatrick, a former professor at Georgetown University, had been scheduled to receive a medal of honor at Barnard, her alma mater, and an honorary doctorate at Smith.

She has been at the center of a national controversy about freedom of speech and the academic tradition of dispassionate discussion since she was heckled and jeered at during an appearance at the University of California at Berkeley Feb. 15.

Her letter said she was "naturally grateful" to the board of trustees at the two colleges and "any others" who supported the awards. "As a faculty member myself," she added, "I feel deeply that a university or college is in the most basic sense defined by its faculty and students."

Kirkpatrick did not elaborate, but her action was an apparent protest against activities by students and faculty members at the two schools. She is scheduled to give a commencement address at Colorado School of Mines in Golden next week, and is expected to give a major speech on academic freedom within the next month, probably on a college campus.

Announcement of the Barnard award touched off a tempest last week at the 2,500-student women's undergraduate division of Columbia University in New York. More than 1,000 students signed a petition protesting the award, the faculty voted its disapproval, 48 to 18, and several seniors said they would be "embarrassed" to accept their degrees while Kirkpatrick was being honored.

School administrators tried to play down the episode last week. Barnard President Ellen Futter said the award was not an endorsement of Kirkpatrick's views but "a tribute to an alumnus who has achieved in an extraordinary way."

Last night a spokesman for Futter said the incident illustrates "a profound need in institutions of higher learning throughout the land for tolerance" and for colleges to remain "open forums" for debate.

A Smith spokesman said the school "respects the ambassador's decision" and "looks forward to having her speak to the Smith community" at the earliest possible time.

Kirkpatrick was scheduled to give the commencement address at Smith, a 2,700-student college in Northampton, Mass., but canceled that appearance after student protests. When school trustees voted to award her an honorary degree anyway, half of the faculty signed a petition disapproving of the action.