Myanmar has been in turmoil since the military overthrew an elected government led by Nobel laureate Aung San Suu Kyi early last year and launched a bloody crackdown on peaceful protests and armed resistance movements that followed.
Noeleen Heyzer arrived in Naypyitaw and was greeted by foreign ministry officials, the army-controlled Myawaddy Television reported late on Tuesday.
Heyzer is expected to meet junta chief Min Aung Hlaing and senior ministers. She will "focus on addressing the deteriorating situation and immediate concerns", the United Nations said in a statement earlier this week.
It did not provide further details of her trip.
A spokesperson for the junta did not respond to requests for comment.
Global condemnation has been heaped on Myanmar's generals, most recently for executing four democracy activists they said had aided "terror acts", referring to attacks by militias fighting military rule and seeking to avenge a deadly crackdown on protests.
Myanmar courts have also handed down long prison sentences to Suu Kyi on what critics say are trumped-up charges aimed at permanently blocking her return to politics.
She was sentenced to six years in prison on Monday after being found guilty in four corruption cases, a source with knowledge of the proceedings said.
The 77-year-old veteran leader has been charged with at least 18 offences ranging from graft to election violations, carrying combined maximum jail terms of nearly 190 years. Suu Kyi has called the accusations absurd and denies all charges against her.
Suu Kyi, who is being held in solitary confinement in a jail in the capital Naypyitaw, had already been sentenced to 11 years in prison in other cases.
Heyzer has not requested a meeting with Suu Kyi, junta spokesperson Zaw Min Tun said on Tuesday.
Zaw Min Tun is expected to hold a routine news conference later on Wednesday.
(Reporting by Reuters staff; Writing by Kanupriya Kapoor; Editing by Lincoln Feast)