The administration of the breakaway Somali republic of Puntland has ordered holders of Kenyan passports to leave within seven days.
Much of Somalia is in ruins after years of fighting
Government spokesman Ahmed Asharo told the BBC that the orders were issued after Kenya's decision not to respect Somali passports.
Correspondents say the order will seriously affect aid agency workers.
Somalia has had no central government for 13 years and Kenya said that Somali passports were being widely forged.
Puntland has declared its autonomy from the rest of Somalia but does not issue its own passports.
Peace talks hit
"We were very surprised by the Kenyan government's move and this is just to remind them that they should have given us time before they made the decision," Mr Asharo told the BBC Focus on Africa programme.
He said the Kenyan directive has delayed the long-running Somali peace talks in Nairobi since traditional elders were unable to travel to join the talks at the weekend.
The Kenyan authorities say the ban, which became effective this month, follows revelations that the Somali passports are no longer being issued in the capital Mogadishu but on the backstreets of Nairobi.
They said forged passports led to security concerns and illegal migration.
The president of Somalia's Transition National Government Abdulkassim Salat Hassan has also criticised the Kenyan directive.
The TNG only controls small parts of the Mogadishu with rival factions battling for domination elsewhere.
Somalia has been without a central government since 1991, when the then president Siyad Barre was ousted.