Three senior Somalia government officials were refused entry at the Jomo Kenyatta International Airport in Nairobi for lacking visas.
The officials were part of a government delegation scheduled to attend the launch of an European Union-sponsored cross-border conflict management programme on Tuesday.
Those denied entry are junior Minister of Water and Energy Osman Libah and legislators Ilyas Ali Hassan and Zamzam Dahir.
The three were, however, holding diplomatic passports.
According to the Somali officials, Immigration officials at JKIA told them that they should have obtained visas at the Kenyan embassy in Mogadishu before proceeding.
The three later told Somalia-based Radio Dalsan that they were told they would have to return to Mogadishu, even though some of their colleagues travelling on foreign passports had been allowed in.
Traditionally, under a bilateral arrangement, diplomatic passport holders are granted entry visas at ports of entry.
"The Kenyan authorities at the airport informed these guys that such plan has changed, and now everyone has to obtain visa from Kenya’s Mission in Mogadishu," a senior Somali official in the delegation, but who travelled on a foreign passport, told the Nation on Monday night.
"The officials learnt this change upon arrival as there was no prior communication regarding this."
While it seems the initial policy towards Somali diplomatic and service passport holders has changed, Mogadishu claims it is not aware.
Reached for comment, Kenya's Foreign Affairs Cabinet Secretary Monica Juma said she was unaware of the details of the incident and suggested that the Somali officials may not have followed proper procedure.
"I would be very surprised if anyone with a valid visa was turned away," she said.
She added that every country has rules on visa and which must be followed to the letter.
This comes barely a week after Kenya Civil Aviation Authority directed flights from Mogadishu to stop over in Wajir for security checks before proceeding to any other airport in Kenya.
KCAA boss Gilbert Kibe said that the move was for security reasons despite protests from Mogadishu.
The officials were travelling for the launch of the programme meant to quell frequent border clashes between communities living near boundaries between Ethiopia, Kenya and Somalia.
EU Foreign Policy Chief Federico Mogherini is due to launch it in Nairobi on Tuesday.