In a statement responding to the Irrawaddy news website's report that it was paying the sum to a former junta general, UNICEF said rents in Yangon were "extremely high" but did not reveal what it was paying.
"We believe that the rent we have negotiated is well under market rates. It is more than we want to pay, but a good deal nonetheless and the best we were able to find," said Myanmar representative Bertrand Bainvel in the statement.
Speaking to AFP Bainvel said the $90,000 sum was "not correct" but declined to provide an exact figure for the office, a purpose-built compound in a leafy upmarket district.
"We will not release (the rental figure) because it is part of the contract that we have, but I can definitely tell you that it was one-third of the market rate. We tried to get the best return on the money," he said.
Sources in the UN and the property market say several UN offices in the city have rents of tens of thousands of dollars a month, including a large complex housing the World Health Organisation.
Responding to the Irrawaddy report that UNICEF had rented its offices from former junta-era agriculture minister Nyunt Tin, Bainvel insisted the organisation had "conducted due diligence" without giving detailed information.
Former junta figures and business cronies have a dominant role in Yangon real estate, with one property agent saying it was "pretty hard" not to rent from them.
Even the European Union has an office in a development which is backed by Asia World, an infrastructure-to-agriculture firm founded by a notorious crony family that was sanctioned by the US government for alleged links to a vast heroin trafficking empire.
"The way you make money here -- precious stones, big business, oil and gas -- these people had connections at some point," said another property market source, explaining the pervasive presence of those with links to the former regime.
Myanmar has undergone dramatic reforms since 2011 under a quasi-civilian government led by President Thein Sein, a former general, spurring the removal of most Western sanctions.
Foreign businesses, lured by the promise of a new frontier market, have begun flowing into the country, while aid groups have also sought to increase their presence.
Property prices in Yangon have soared as demand vastly outstripped supply.
But the alleged UNICEF rent was much higher than those thought to be paid by other UN agencies, according to the estate agent.
"If it is $90,000 or $80,000 then it just seems too high," he said, adding that he had not seen the property first-hand.
The organisation, which has 130 staff in Yangon, moved into the offices in mid-2013 after it was asked to vacate space in a prominent downtown hotel that had been home to a number of UN agencies for years.