The UN leadership in Myanmar tried to stop the Rohingya rights issue being raised with the government, sources in the UN and aid community told the BBC.
One former UN official said the head of the UN in Myanmar (Burma) tried to prevent human rights advocates from visiting sensitive Rohingya areas.
More than 500,000 Rohingya have fled an offensive by the military, with many now sheltering in camps in Bangladesh.
In the month since Rohingya Muslims began flowing into Bangladesh, the UN has been at the forefront of the response. It has delivered aid and made robust statements condemning the Burmese authorities.
But sources within the UN and the aid community both in Myanmar and outside have told the BBC that, in the four years before the current crisis, the head of the United Nations Country Team (UNCT), a Canadian called Renata Lok-Dessallien:
One aid worker, Caroline Vandenabeele, had seen the warning signs before. She worked in Rwanda in the run-up to the genocide in late 1993 and early 1994 and says when she first arrived in Myanmar she noticed worrying similarities.
"I was with a group of expats and Burmese business people talking about Rakhine and Rohingya and one of the Burmese people just said 'we should kill them all as if they are just dogs'. For me, this level of dehumanisation of humans is one sign that you have reached a level of acceptance in society that this is normal."
for more than a year I have been corresponding with Ms Vandenabeele, who has served in conflict areas such as Afghanistan, Pakistan, Sri Lanka, Rwanda and Nepal, where she is now based and where we recently met.
Between 2013 and 2015 she had a crucial job in the UNCT in Myanmar. She was head of office for what is known as the resident co-ordinator, the top UN official in the country, currently Ms Dessallien.
The job gave Ms Vandenabeele a front-row seat as the UN grappled with how to respond to rising tensions in Rakhine state.
Back in 2012, clashes between Rohingya Muslims and Rakhine Buddhists left more than 100 dead and more than 100,000 Rohingya Muslims in camps around the state capital, Sittwe.
Since then, there have been periodic flare-ups and, in the past year, the emergence of a Rohingya militant group. Attempts to deliver aid to the Rohingya have been complicated by Rakhine Buddhists who resent the supply of aid for the Rohingya, at times blocking it and even attacking aid vehicles.