The government then issued a permit for the bear to be shot and killed.
That did not go down well with Lithuania's hunters who refused, aware that there is only a tiny number of the protected species in the entire country.
The Lithuanian Association of Hunters and Fishermen said it was shocked by the government order.
The association's administrator, Ramutė Juknytė, told The Associated Press on Wednesday that the bear was a beautiful young female who was about 2 years old and did not deserve to be shot. “She was scared but not aggressive. She just didn’t know how to escape the city but she didn’t do anything bad,” he said.
The organization tracks the movements of bears. It believes there is only five to 10 bears in the Baltic nation, but does not have a precise number.
The drama began on Saturday when the bear entered the capital. It was the first time in many years that a bear had entered the city and it became a national story. The animal came within about 4-5 kilometers (about 2-3 miles) of the city center.
Since causing a stir with their permit to kill the bear, Lithuanian authorities have been on the defensive.
Deputy Environment Minister Ramūnas Krugelis said that a kill permit was issued purely as a precaution in case the bear posed a threat, according to a report by the Lithuanian broadcaster LRT.
The hunters proposed a more humane approach: sedation, tracking and relocation.
As the debate over the bear's fate unfolded, she took matters into her own paws and wandered out of the city.
Juknytė said that the bear was recorded by a camera on Wednesday, peacefully wandering through a forest some 60 kilometers (40 miles) from Vilnius while munching on corn.
Brown bears are native to the region and were once common. They were wiped out in Lithuania in the 19th century due to hunting and habitat loss.
In recent years they have started reappearing in small numbers, typically wandering in from neighboring countries like Latvia and Belarus, where small bear populations still exist. Bears are protected under Lithuanian and EU law as they are considered a rare and vulnerable species in the region.