"Most schools in the northeast depend on teachers from other parts of the country," Mohamed Sheikh, a teacher from the Mandera secondary school, told The Anadolu Agency.
"We have virtually no indigenous teachers," he said. "We are facing a major crisis."
A total of 920 teachers have failed to report back to their respective schools in Mandera, Garissa and Wajir counties since public schools reopened their doors following a 40-day Christmas and New Year holiday.
Schools were supposed to reopen on Jan. 5, but the resumption was delayed due to a teachers' strike.
Classes eventually resumed on Jan. 19 and teachers in the north were expected to report back to their schools last Monday after security arrangements had been made.
But non-indigenous teachers never came back, complaining of rampant insecurity in the region.
Since 2011, northeastern Kenya, which shares a border with Somalia, has witnessed a series of attacks by Al-Shabaab.
Exploiting the long and porous border, Al-Shabaab has mainly carried out limited grenade and shooting attacks on northern towns.
On Nov. 22, Al-Shabaab militants hijacked a Nairobi-bound bus in Mandera, killing 28 people aboard, all non-Muslims, including 23 teachers.
A month later, 36 quarry workers, all non-indigenous, were killed by Al-Shabaab.
"We lost five teachers from my county," William Lukoye, a teacher at the Mandera Primary school who hails from Mumias County in western Kenya, told AA.
"These were our kinsmen. I am traumatized. We are all traumatized," he said. "There is no way you can tell me to go back."
"We have been silent for many years," Lukoye fumed. "The killings last year were only a climax."
He insisted that the government was aware of their complaints but had never taken them seriously.
Thousands of students have been caught in a tug-of-war between the country's teachers' union – which has urged teachers not to report back to the region – and the government.
The government, meanwhile, has threatened to sack all teachers who have not reported back to work by Feb. 2.
An emergency meeting was convened by the government in Nairobi on Wednesday to address the issue.
"Teachers should not go back to school until all aspects are resolved," National Teachers' Union Secretary-General William Sossion told AA after the meeting.
"I will repeat it again and again. Let the government dare sack any teacher come Monday," he said in Swahili, the national language.
"I dare them to sack one teacher," Sossion thundered. "They will face our fury."
Besides insecurity, the union has also complained about alleged discrimination, sexual harassment and the forced conversion to Islam of non-indigenous teachers.
A 2009 census puts the population of the three affected counties at approximately 2.4 million, mostly Muslims of Somali origin.
"I think the teachers' union's allegations are out of this world," Aden Dualle, an MP from Garissa and parliament majority leader, told AA.
"They have hijacked the whole situation, despite the government assuring security for teachers in northern Kenya," he said.
"I call upon all teachers to report to their respective schools by Monday," he urged.
Police now want to question Sossion over "threats" he allegedly made to teachers' main employing body, the Teachers Service Union.
In Garissa, the region's largest city, the local chapter of the Kenya Secondary School Heads Association announced it would take Sossion to court for alleged incitement of non-local teachers.