A senior UN official was cleared of sexual harassment earlier this year because the secretary general rejected the verdict of an internal watchdog.
Mr Annan decided the case against Lubbers was "unsustainable"
High Commissioner for Refugees Ruud Lubbers, 65, a former Dutch prime minister, escaped censure in July when Kofi Annan dismissed a complaint.
But a revised report issued by UN watchdogs on Thursday revealed that investigators supported the allegation.
Mr Annan refused to take action, saying the allegations were "not sustainable".
Mr Lubbers was cleared of improper conduct after a 51-year-old woman on his staff claimed he had groped her.
The UN's Office of Internal Oversight Services investigated the complaint and backed the woman's complaint, it has now been revealed.
In addition, the internal investigation recommended that "appropriate action" was taken.
Despite the recommendation, Mr Annan dismissed the complaint, but instead wrote to Mr Lubbers stressing his concerns "in the strongest terms".
UN spokesman Fred Eckhard attempted to explain the secretary-general's verdict on Thursday, asserting that Mr Annan decided the allegations were unsustainable after seeking legal advice on the matter.
"He did not say there was no evidence. He said he found the evidence unsustainable on a legal basis," Mr Eckhard said.
The investigation centred on allegations that Mr Lubbers and an unnamed manager at the UN High Commission for Refugees sexually harassed a woman on a total of three occasions.
The disclosure that the OIOS ruled against Mr Lubbers was made public when "technical reasons" meant that details of the case were included in a version of the watchdog's annual report.
Lubbers denied he had been involved in any improper behaviour
An original version of the report did not include details of the case against Mr Lubbers, recording only that investigators "submitted a report to the secretary-general on the allegations".
In the revised version, the watchdog "submitted a report to the secretary general supporting the allegations and recommended that appropriate actions be taken accordingly."
In May Mr Lubbers acknowledged making a "friendly gesture" which was misunderstood by the woman.
He denied allegations of improper conduct.