Nearly a month after his death, Jeffrey Epstein continues to haunt some of America’s most prestigious institutions.

On Saturday, a prominent figure at the Massachusetts Institute of Technology stepped down after the disclosure of his efforts to conceal his financial connections to Mr. Epstein, the disgraced financier who killed himself in a Manhattan jail cell last month while facing federal sex trafficking charges.

Almost immediately, the M.I.T. official, Joichi Ito, left the boards of three other organizations: the MacArthur Foundation, the John S. and James L. Knight Foundation, and The New York Times Company, where he had been a board member since 2012. He also left a visiting professorship at Harvard.