The government is yet to make a policy that guides taxation and licensing by counties and the national government.
Multiple taxation and licensing by the two levels of government has been blamed for making it difficult to do business in Kenya.
East African Community Principal Secretary Kevit Desai said the country was yet to develop a national policy to harmonise the different levies imposed by counties and national agencies.
But the PS said the ministry has taken the first step in formulating a policy that would protect small and medium-sized enterprises (SMEs) and manufacturers from exploitative levies.
Dr Desai said the many levies were against the government's agenda of promoting ease of doing business, and that a national policy would be developed after a series of meetings with county governors and SMEs.
The PS on Thursday held a meeting in Eldoret with Kenya National Chamber of Commerce and Industry (KNCCI) officials, Kenya Revenue Authority (KRA) officers and Uasin Gishu Governor Jonathan Bii in Eldoret.
He said the meeting was aimed at listening to stakeholder views on the matter.
Among punitive levies was the payment of cess, where traders said they were paying to many counties along the major highway from Mombasa to the Kenya-Uganda border and other borders.
The PS was told that counties and authorities such as KRA, National Environment Management Authority and Kenya Bureau of Standards were all charging various levies, making it difficult for businesses to thrive and create jobs.
"The county levies and other taxes are still punitive and the private sector wants harmonisation," Dr Desai said.
"There is no national policy on harmonisation of these levies so far, but we have taken the bold step of listening to stakeholders."
KNCCI Uasin Gishu branch Chairman Willy Kenei said harmonisation of levies would spur the expansion of business and the creation of more jobs.
He cited clearance of goods at the borders, saying it was taking long.
"Each county is charging for different licences and this is making it hard to do business," he said.
"Eldoret will soon become a city and we want to expand the business to make use of the Eldoret International Airport."
