"There are some unnecessarily extra restrictions and discriminations against health workers. These people are ... risking their own lives," Ban told a news conference in Vienna.
Without naming any country, Ban said that these "unnecessarily strong and strict restrictions" included "quarantine for health workers ... not based on science and medical evidence".
"That is my honest and urgent opinion to the international community," he said, stressing however that people with Ebola symptoms "should be immediately treated and supported".
Experts say quarantining medical professionals who have shown no symptoms of the virus is counter-productive and could deter other workers from helping contain west Africa's Ebola crisis.
In a case which attracted international criticism, New Jersey Governor Chris Christie kept a nurse in an isolation tent for three days after she flew back from Sierra Leone.
Meanwhile Canada and Australia controversially announced last week that they were suspending visa applications from Ebola-hit west African nations.
Almost 5,000 people have been killed by Ebola, according to the World Health Organization, which has recorded more than 13,000 cases but admits the real number of could be could be much higher.
Ban was speaking at a UN conference of developing landlocked countries in the Austrian capital.