During a Friday briefing with reporters, Dr. Catherine Elliott, the territory's acting chief medical officer of health, reaffirmed that schools would remain open for the time being.
"The level of risk in schools is acceptable, and I'm confident in the decision of students return to classrooms this year," she said.
"I'm monitoring the situation carefully, and I'll continue to work very closely with the Department of Education in the best interest of students, staff and administration."
That affirmation comes on Friday, after at least two schools moved to remote learning this week.
Most students at Porter Creek Secondary School went online after 18 teachers were absent, half of those for reasons related to COVID-19. Nicole Morgan, deputy minister of education, said the school found five substitutes but ultimately couldn't keep the doors open.
The Department of Education said Nelnah Bessie John School in Beaver Creek also began remote learning, as both teachers were unable to be in the classroom.
Morgan, who was also part of the briefing on Friday, said "it will likely be for operational challenges that we will experience disruption to our school environments."
"We know that Omicron is going to present to us new challenges in particular around staff absenteeism," Morgan said.
"We can expect that with with the ongoing increasing cases ... that curve will will be steep and we can expect that we will see these types of — for lack of a better word — rolling, remote learning."
Morgan said there are two factors into the decision on keeping schools open. One is the level of risk to public health. The other is whether staff shortages make it hard to keep the school open. She added that the school is ready to support students who choose to learn from home.
She said if schools do have to go to remote learning, it will be for "as short a period of time as we can."
Robert Service School in Dawson City also asked to delay in-person classes in a Facebook post Tuesday, over concerns of the Omicron variant of COVID-19 spreading over the holidays.
Morgan said Friday the department is working with the First Nation government school council, the school principal, and the superintendent on the request.
Low attendance in Dawson
During a news conference Wednesday, Premier Sandy Silver had said that "schools should be the last thing to close down in a pandemic."
He added that when the state of emergency was declared last November, the territory strengthened public health measures in schools, including requiring students to wear masks at all times when inside schools."
However, some Yukoners seemed hesitant to send their child back to school in-person.
In Dawson City, only 42 of around 215 students attended school on Tuesday (according to the Yukon government — the school's Facebook page says it had 36 students in attendance with nine staff away, "most because of the 'stoplight' measures").
Silver pointed to the frigid weather as one possible reason for the low attendance.
A post from Robert Service School said teachers this week would be "reviewing previously covered learning or extended learning opportunities."
"The remainder of the week will not involve coverage of new material," the post read. "High school students are starting revision of the first semester's work in anticipation of the upcoming examinations next week."
Heating issues at Haines Junction school
Meanwhile, Saint Elias Community School Council in Haines Junction issued a written notice to families Wednesday that the school was short 13 staff and the heating system wasn't working properly. In parts of the school, it was only 13 C inside, said Cassandra Wheeler, chair of the school's council.
She told CBC News this week that the council had asked the Department of Education to move to at-home learning for the week, but the request was denied.
"It's too cold to be safe in the classroom," she said. "They're not going to be able to focus. If we have a severe teacher shortage, how are teachers and EAs going ot support our students that are actually there?"
During the Friday briefing, Morgan said there were no frozen pipes, no fuel lines that were not working, and just one of the three boilers used in the heating system at the school was affected by cold temperatures.
She said space heaters were used to ensure that the school remained safe for staff and students and that work was being done to address the issue, and it continues to be monitored Friday.
"The temperature in the school is fine for learning," Morgan said.
She said conversations are also ongoing as to whether "there a public health reason for the school to be closed."