The secretary-general was "convinced that [the resignation] is in the best interest of UNHCR, its staff and the refugees it serves that the page be turned and a new chapter be started," according to a statement issued by his spokesman on Sunday.
Although Annan acknowledged he initially had accepted legal advice that the allegations were unsubstantiated, "the continuing controversy has made the high commissioner's position impossible," the statement said.
Annan thanked Lubbers for "the devotion and the commitment he has shown" to helping refugees over the last four years.
Allegations first surfaced last year that Lubbers had made unwanted sexual advances toward a female employee.
An investigation by the UN watchdog concluded that Lubbers engaged in sexual harassment, but Annan rejected its conclusion on grounds it could not be legally sustained.
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