Mr Joho claimed Jubilee was plotting to gag critics of high-level graft in the national government with charges of hate speech.
The governor also criticised Mr Ruto, who has been vocal in defending Jubilee regarding the reported scandal at the Ministry of Health. He claimed the national government continued to procure medical equipment for county governments in order to create an avenue to loot public money.
On Saturday, Ruto dismissed Opposition criticism and alleged that key Opposition leaders plundered public money and failed to use resources to develop the country during the grand coalition government of 2007- 2012.
"We all know that Jubilee is the most corrupt government that has ever been in existence since independence and now President Uhuru Kenyatta is threatening to gag and arrest anyone criticising the Government concerning graft. He should know that we are not afraid of prison and if it comes to that, Mr Ruto should be the first one to be investigated over graft," Joho said during a fundraiser at Shika Adabu Primary School in Likoni on Saturday evening.
But in a quick rejoinder, Ruto's spokesman David Mugonyi yesterday dismissed Joho, describing him as a politician afflicted by an "inflated ego" and "fragile education", and accusing him of attacking the Deputy President in order to raise his political status and "please his ODM masters".
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Mr Mugonyi threatened that Ruto would sue anyone who associated him with corruption.
"Mr Joho has a penchant for attacking the Deputy President and a misguided sense of belief that by doing so, he will elevate his fragile education and please his masters in ODM," said Mugonyi.
He told the governor to find "better and civil ways to raise his political profile".
Joho demanded an investigation, saying Ruto's aides were mentioned in financial scandals. He questioned how the Government spent Sh100 million to procure containers for clinics, which he argued should have cost Sh2 million each instead of the quoted Sh10 million.
The governor said health was a devolved function yet there was no consultation with the county health department about the containers.
"The purchase of these containers is another scam. First they procured over 100 containers at a cost of Sh10 million per container but the original price was Sh2 million. No one was consulted at the county level while procuring the containers yet we know Health is devolved," said Joho.
Mombasa Woman Rep Mishi Mboko, who is eyeing the Likoni MP seat, said ODM was the most suitable party to see Raila become President.