The restaurant fell into the spotlight of city authorities after furious residents took to social media to denounce an apparently racist policy of not allowing African patrons to eat there after 5 pm.
The owners of the restaurant said the measure had been put in place following a robbery in 2013, and have apologised for causing any offence, the Daily Nation reported.
But it said the Chongquing Chinese restaurant, situated in Nairobi's bustling commercial and residential district of Kilimani, had been shut down anyway for not having the proper licences.
He also said that "all business and service providers must ensure that all customers and clients are treated with respect and dignity, irrespective of race colour, sex, tribe and religion," the Standard newspaper quoted him as saying.
Reports said the restaurant's Chinese owners and managers had also been summoned by Kenya's immigration authorities.
A city official however told the Star newspaper that the incident "has nothing to do with the friendship and diplomatic relations Kenya enjoys with China," a major investor in east Africa's biggest economy.