In a report to the Council on Friday, Lee said she believes that events in northern Rakhine "bear the hallmarks of genocide" based on interviews she had with Rohingya living in displacement camps in Bangladesh.
Tirana Hassan, Amnesty's crisis response director, said: "The remaking of Rakhine State is taking place in a shroud of secrecy".
In Kan Kya village, for example - burned down between August and November a year ago - homes and at least two mosques were demolished to make way for a new security force base. At least three new such facilities are reportedly under construction.
The village demolitions and evictions of Rohingya that are still in Rakhine - it is estimated that by August y lived around one million - to give room to new constructions have multiplied since beginning of year, says AI.
In one instance, the group found, a new border police post was recently built near what used to be a mosque.
Though admitting the images only paint a partial picture, the rights group says structures for security forces, helipads and even roads have been built in and around torched Rohingya properties.
Almost 700,000 Rohingya Muslims have fled to neighboring Bangladesh since fighting broke out between Rohingya militants and Myanmar's security forces last August.
Delivering her report to the Council in Geneva yesterday, Lee said that to date accountability for the crimes committed in Rakhine State following August 25 past year, and October 9, 2016, was elusive, adding that this must now be the focus of the global community's efforts to bring long-lasting peace, stability and democratisation to Myanmar.
Nearly six months after launching the military operation, Myanmar's military has admitted to only killing 10 captured Rohingya men, who, it claims, were "terrorists".
The largest of the new bases is in the village of Ah Lel Chaung in Buthidaung Township, where eyewitnesses said that the military forcibly evicted Rohingya people from certain areas to make way for construction.
Amnesty said that authorities were also destroying villages not burnt but "deserted by inhabitants fleeing killings, starvation and the threat of further violence".
The images also show new refugee reception centres surrounded by the new security fences and a heavy presence of military forces, raising concerns that Myanmar is preparing to restrict the freedom of the Rohingya refugees returning home to safety.
"Not only are their homes gone, but the new construction is entrenching the already dehumanizing discrimination they have faced in Myanmar", Hassan added.
Myanmar's military had also advanced into Mutraw District in Kayin State, an area controlled by the Karen National Union, despite a ceasefire agreement, she said.
Repatriations were scheduled to begin during the fourth week of January, but have yet to start on account of various delays for which officials from each side have blamed the other.
This is worrying since authorities have in the past resettled members of other ethnic groups into Rakhine State as part of efforts to develop the region.