“I could spend the rest of my life figuring out how Harvard could announce $5 million for Boston and not know how damaging that would be to our relations,” he said. “You have to put that behind you.”

“Cynics at Harvard need to know we can say thank you,” he added. “Cynics on our side need to know that Harvard can give.”

City officials have praised the summer academy as a specific program where the University can share accountability over improving students’ learning.

At the event yesterday, Superintendent of Schools Bobbie J. D’Alessandro said the summer academy was “a dream become a reality.”

“Isn’t it so much better when we’re partners?” said City Manager Robert W. Healy at the announcement.

University officials attributed the bad feelings of earlier this spring to Cambridge officials who compared the Boston afterschool program to the Cambridge summer school venture.

“I think the reaction was not to this program,” said Mary H. Power, senior director of community relations for Harvard.

She said the Cambridge initiative was not meant to balance out Harvard’s commitment to Boston and said the timing of the Boston announcement that had angered the Cambridge city councillors was “coincidental.”

—Staff writer Imtiyaz H. Delawala contributed to the reporting of this article.

—Staff Writer Andrew S. Holbrook can be reached at holbr@fas.harvard.edu.