The Foreign Affairs Ministry has maintained that county officials have to adhere to the new US visa rules.
The visa issue is a centre of a protracted battle between the two tiers of government lately.
Governors on March 1 said they will sue if the ministry fails to help them get visas to travel to the United States.
In a statement, CS Amina Mohamed on Friday said the decision, which she termed as straightforward, is a sovereign one taken solely by the US government.
She said the A Visa Category are a preserve of officials travelling on behalf of the national government and their immediate family members – namely spouses, unmarried sons, and daughters.
"County government officials travelling for official duties on behalf of the national government qualify for official visas," Amina said.
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"County officials travelling to the United States exclusively on behalf of their county governments do not qualify for official visa status, whether they are traveling on diplomatic passports or regular passports," she said.
The CS said that such officials must follow normal visa procedures and cannot be granted official visa status.
"They must be interviewed, provide fingerprints and pay application and issuance fees," Amina said in the press statement.
The ministry posits that all county officials, except those traveling on behalf of the national government, will be issued with B1/B2 visa category within 10 business days prior to the date of travel.
The said visas do not require a diplomatic note from the Ministry of Foreign Affairs.
"Governors and their immediate family members traveling on diplomatic passports, however, are exempt from fees, regardless of whether they are traveling for national or country business, although they must appear at the embassy to provide fingerprints," Amina said.
The CS added that the decision is backed by Article 41 (2) of the Vienna Convention on Diplomatic Relations of 1961.
"All official business with the receiving state entrusted to the mission by the sending state shall be conducted with, or through the Ministry of Foreign Affairs or the receiving state or such other ministry as may be agreed," the regulation states.
Foreign Affairs ministry reminded governors to understand that applications and issuance of visas are a prerogative of any issuing state.
"In practice and in fact, considerations for issuance or denial of visas irrespective of category remains a sovereign right of the issuing state," Amina said.
The visa row emerged when Mombasa Governor Hassan Joho travelled to the US amid allegations that his allies were linked to trade in narcotics.
The governor returned to the country on Sunday last week.
The tour came hot on the heels of the and two foreigners to America on charges of running an international drug trafficking syndicate.
On February 14, the Foreign Affairs ministry wrote to the counties indicating that the US Embassy in Nairobi will no longer issue official visas (category A).