Kenyan trade unions have urged non-Muslim public sector workers including teachers and doctors to leave the country's lawless northern region, site of two deadly attacks by militants in the past two weeks, because of the security risks.

Somali militant Islamist group al Shabaab killed 36 non-Muslim workers on Tuesday at a quarry in northeast Kenya. They also shot dead 28 non-Muslim bus passengers on November 22 while sparing Muslim travellers.

Many of the public sector workers in less prosperous northern Kenya are Christians who moved from the Rift Valley in the west, lured by promises of more work.

"They (the authorities) must guarantee the safety of workers," said Wilson Sossion, secretary-general of the teachers' union and also general secretary of Kenya's Trade Union Congress.

He said the unions' call was addressed to 10,000 teachers and 6,500 other public servants, including doctors and nurses.

The governor of northeast Kenya's Mandera county, Ali Roba, implored the workers to stay put, saying an exodus would only deepen the area's isolation from the rest of the country. As it is, the region struggles to attract qualified workers, he said.

"It's unfortunate that the likes of the Kenyan National Union of Teachers is going on the media to say civil servants who are non-Muslim should leave," he told Reuters. "Terror is terror, it's affecting us equally."

The exodus has already started, though Sossion said he did not know how many workers had so left Mandera.

"People are scared," said Ken Mulinga, a clinical officer originally from western Kenya who fled Mandera this week after spending five years in the region. "The best thing for now is to leave that place and watch from a distance."

President Uhuru Kenyatta, under pressure to do more to curb the incessant militant attacks which have killed more than 200 people since 2013, announced a shake-up of his security team on Tuesday after the killing of the quarry workers.

Al Shabaab says it will keep up its attacks to persuade Kenya to pull its troops out of Somalia, where its forces have joined other African Union troops battling the militants.