Kenya says it will register undocumented Burundians and other East Africans living in the country, following days of anxiety over President William Ruto's directive targeting foreigners in small-scale businesses.

On Monday, hundreds of Burundians scrambled to process travel documents amid uncertainty over whether they could remain in Kenya.

Charles Owino, the Kenyan government spokesperson, has now said those without proper documents should register through their embassies or high commissions as the authorities work with diplomatic missions to regularise their status.

Those undergoing registration would be presumed legally in Kenya during the process, Owino said.

Ruto had set Monday as the deadline for foreigners operating small-scale businesses to cease work. The directive came after the trade ministry said some foreigners exploit visa rules to work without the required permits.

Long queues were seen outside Burundi's embassy in the capital, Nairobi, after it said it would offer free emergency travel documents to citizens who wanted to go back home.

Others were seen racing to buy bus tickets.

Some Burundians have reportedly faced hostility after President Ruto ordered action against foreign street vendors and those operating small shops, saying such jobs should be protected for Kenyans.

Kenyan officials have since sought to reassure neighbouring countries that there is no blanket ban on foreign traders.

Addressing a news conference on Monday, Owino said the government had opened registration and documentation of all foreign nationals residing in Kenya without valid documents.

He acknowledged that because of historical circumstances and regional dynamics, a number of East African nationals, including several Burundians, resided and operated in Kenya without full documentation.

"To address this constructively, the government of Kenya is establishing a formal documentation and registration window," Owino said.

"We call upon all undocumented East African community nationals, and specifically Burundian citizens currently residing in Kenya, to immediately present themselves to their respective high commissions or embassies for formal identity registration."

In a statement on Tuesday, the Kenyan government said foreign nationals running businesses had 90 days to regularise their immigration status, work permits, business registrations and licences.

After that the requirements would be "enforced firmly and strictly", it said.

"During this period, the responsible government agencies will provide the necessary guidance and administer the applicable requirements fairly, consistently and without discrimination," Kenya State House's statement added.

It also warned that no individual or group had "the authority to harass, intimidate, threaten or interfere with foreign nationals or their businesses".

Senior Kenyan foreign affairs official Korir Sing'oei has apologised to Burundians over the harassment some have faced, saying the president's directive had been misunderstood.

"I want to say sorry to all the Burundi nationals here," Sing'oei said during a visit to the Burundian embassy in Nairobi on Monday.

He said the government would tighten security in areas where Burundians live.

Kenya hosts hundreds of thousands of migrants from across East Africa seeking work and business opportunities.

According to the United Nations refugee agency, there are around 16,000 Burundian refugees and asylum seekers in Kenya.

It is unclear how many are involved in small-scale trading.

On Monday, some of them were seen carrying all their belongings - from suitcases to mattresses - as they tried to leave Kenya. However, some of them said they could not afford the cost of travel and urged the Kenyan government to extend the deadline.

Read More