The Health Board is recommending children switch to distance learning next week in areas with a high level of coronavirus.
The agency sent a letter to local governments on Thursday.
"We appealed to the municipalities which have a high level of infection in the area. We recommended that the municipalities switch to distance learning in these schools between February 14 to 18, ie next week," Margit Kallas, the head of the Northern Region of the Health Board, told ERR.
She said the branches of the agency in the southern, western and eastern regions made similar recommendations.
Kallas did not agree when asked that the rate of infection is declining in the young and rising among the elderly.
"When I talk about the northern region, where I lead the team, according to our data, the highest infection rate is still among school-age people. True, it has started to increase among those over 60, and last week it was 35 percent in the northern region," she said.
The official said the rates are still high among school-age children and people who work in educational institutions.
Speaking about Tallinn, she said the rates are highest in Lasnamäe, Mustamäe, the Kesklinn, Põhja-Tallinn and Haabersti. Kallas said distance learning should be considered in schools in these areas where a lot of people are ill.
Municipalities are still discussing the issue and only Saue municipality has responded in the northern region so far, she added. Schools will be able to organize their own setup.
Minister of Education: Restrictions must be well justified
Minster of Education Liina Kersna (Reform) was not pleased with the Health Board's decision which she said came as a surprise.
She told ERR the plan had not been discussed at yesterday's meeting with the government or raised by the Health Board before.
"I continue to believe that schools should be sent to distance learning depending on the specific situation at the school, which is based on the spread of the virus in that specific school," she said.
School children continue to undergo regular rapid testing and Kersna said only 12 whole schools out of 521 are currently distance learning due to the spread of the virus. There are 113 carrying out hybrid learning.
"Throughout the coronavirus crisis, we have come to a common understanding that we must not unduly restrict children's right to education. Restrictions must be well justified," she emphasized.
Mayor of Tallinn criticizes recommendations
Mayor of Tallinn Mihhail Kõlvart (Center) criticized the recommendations and the failure of state agencies to agree on a unified policy. He said Tallinn may not send all schools to distance learning on Monday.
He called the plans "confusing", especially as Tallinn's plans to send some schools to online learning have been criticized.
Kõlvart also questioned why the government and Health Board cannot agree, with the agency saying one thing and the Ministry of Education another.
The mayor said that there is still no coronavirus strategy and this means there is no understanding of how to behave in different stages of the pandemic.
"What do local governments have to do now if our operational decisions cause resentment at the state level, but at the same time the state's own messages are not coordinated and even communicated with each other?" Kõlvart asked.
He also doubted the data cited by the Health Board about different regions of Tallinn. Kõlvart said the city government will not rush to implement the recommendations on Monday.
"We have a meeting with school leaders on Tuesday, we are discussing the situation, we have been discussing it every week and reacting to the situation. I remind you once again that schools have already implemented distance learning in one way or another," said Kõlvart.
Editor: Helen Wright