John Ogutu was arrested at his business premises for acting as an SGR ticket booking agent without a license.
He was detained at the Miritini terminus police where he recorded a statement before being released on a Sh20,000 police bond.
Police officers handling the case said Ogutu will be taken to court on Monday where he will be charged.
But social media users denounced the arrest through the #IStandwithWasonga.
The argument among the commuters is that the vendor saves them the hustle of having to get the SGR tickets.
Ogutu's business is to deliver the Sh700 tickets to the commuter's doorsteps, a move that was hailed by many Kenyans.
Buses charge Sh150 from the Mombasa CBD to the terminus at Miritini.
Those who intend to use SGR spend hours on traffic at Kibarani bridge, a situation which they say makes them susceptible to miss tickets.
Ogutu, in an earlier interview, said his clients book the tickets through Mpesa and his job is to physically deliver them to the owners.
But Achoki asked: "Why should you deliver them to people who want to go at a cost?"
He said the government wants Kenyans to pay Sh700 to use the train from Mombasa to Nairobi in the economy class.
"That was the pronouncement. Until that pronouncement is reviewed, Kenyans should not pay more than Sh700 on the SGR."
The directive was issued by President Uhuru Kenyatta during the launch of the SGR passenger service on May 31.