Attackers killed nine police officers on Oct. 9 in a coordinated assault on posts near Myanmar's border with Bangladesh. Authorities say members of the Rohingya minority carried out the attacks and launched a security sweep.
Since then, at least 86 people have been killed and the United Nations says about 34,000 civilians have fled across the border to Bangladesh.
Residents and refugees accuse the military of killing, raping and arbitrarily detaining civilians while burning villages in northwestern Rakhine State.
The government led by Nobel Peace Prize winner Aung San Suu Kyi denies the accusations and insists a lawful counter-insurgency operation is underway.
Lee would visit the north of Rakhine State, where the military operation is taking place, the commercial hub Yangon, the capital Naypyidaw and Kachin State in the north, where government forces are battling autonomy-seeking ethnic Kachin guerrillas, the Office of the United Nations High Commissioner for Human Rights said in a statement.
"The events of the last few months have shown that the international community must remain vigilant in monitoring the human rights situation," in Myanmar, Lee, the U.N. special rapporteur on human rights in Myanmar, said in the statement.
Suu Kyi, a former political prisoner and champion of democracy in then military-ruled Myanmar, came to power in April after a landslide election win, installing her confidant, Htin Kyaw, as president.
However, increasing violence in border regions has raised questions about Suu Kyi's commitment to human rights and ability to rein in the military, which retains a major political role.
The government has restricted aid to northern Rakhine State, where most people are Rohingya Muslims denied citizenship in Myanmar, and prevented independent journalists from visiting.
Muslim-majority Malaysia and Indonesia, which has the world's biggest Muslim population, have raised concern over the Rakhine crisis, which security officials believe is attracting the attention of international militant groups.
Lee will also investigate the impact on civilians of intensified fighting between the army and rebels in Kachin and Shan states, which she said "is causing some disquiet regarding the direction that the new government is taking in its first year of administration".
Aye Win, U.N. spokesman in Myanmar, said Lee had arrived in Myanmar late on Sunday and was due to fly to the Kachin State capital of Myitkyina on Monday.
Presidential spokesman Zaw Htay said the government would provide Lee with security to visit conflict areas.
Zaw Htay also said a Myanmar government delegation would visit Bangladesh on Jan. 11-13 to discuss the situation on the border.
The neighbors' relations have been tested by the stream of new refugees entering Bangladesh and by reports that Myanmar's navy has shot at Bangladeshi fishermen.