The details of the investigation by the UN's office of internal oversight services (IOS) were first reported by the Brazilian daily newspaper O Estado de S. Paulo.
The case concerns allegations made against UNAIDS deputy executive director Luiz Loures by a female employee, who claimed that Loures harassed her on multiple occasions beginning in 2011 and assaulted her in a lift in 2015.
The IOS determined that there was insufficient evidence to support the woman's allegations, but criticized Sidibe for his attempt to set up a meeting between the accuser and Loures to solve the dispute quietly.
The IOS "found it perplexing that Dr. Sidibe stated that he approached (the accuser) in an attempt to resolve the matter informally, given the Dr. Sidibe was aware at the time that the matter was under official investigation by IOS", the internal report said.
The criticism of Sidibe comes amid heightened scrutiny of sexual misconduct within the world body, triggered by the #MeToo movement born in the wake of the allegations against film producer Harvey Weinstein.
Campaigners from Code Blue, part of the AIDS Free World civil society group, said in a statement this week that the case was "grossly mishandled", in a statement co-authored by former UN HIV/AIDS special envoy Stephen Lewis.
Code Blue raised particular alarm over a quote in a UNAIDS press release saying that in cases of sexual harassment investigations "the final decision-maker in such matters is the UNAIDS Executive Director".
They called the case "a double assault -- the first by a high-level assailant, and the second by a so-called investigation", noting that Sidibe was both a witness and the final judge.
But a UNAIDS spokesperson told AFP that Code Blue's allegations were "not correct".
"In a situation like this the executive director would normally recuse himself" because of the clear conflict of interest in serving as both a witness and a judge, the spokesperson said.
Such recusals are "best practice and is what was applied in the case you're referring to", the spokesperson added.
The spokesperson also said that IOS concerns over Sidibe's role in the probe had not triggered a separate review but they had been brought to his "attention".