Muhuri Chairman Khelef Khalifa and rapid response officer Francis Auma have been arrested.
The two were arrested for demonstrating against motorists being forced to use M-Pesa to pay for ferry services at the Likoni crossing channel.
Kenya Ferry Services partnered with Safaricom and introduced M-Pesa toll payment.
Motorised ferry users are to dial *721# to pay their toll charges.
Khalifa, who led protests on Thursday against KFS, said the management is violating ferry users' right of choice.
He noted that a public entity cannot force people to use a private entity, even against their will.
"This is not right. Why is the KFS forcing people to have only Safaricom lines? Are they in business against the other service providers?" Khalifa posed.
However, KFS communication officer Aaron Mutiso said refuted claims that there has been bias in terms of mobile payment as motorists have been forced to pay using M-Pesa.
Mutiso said the management has been in discussion with Airtel and they were finalizing on the process of acquiring their codes.
“The process is almost done and soon it will be unveiled. Ferry users have been patient, and we ask them to remain patient for a few more weeks,” he said.
Mutiso further said the Mpesa services have not in any way discriminated against other mobile users as it is being claimed by the rights group.
He noted that the KFS management has its staff, who have Safaricom lines and assist other mobile services users or foreigners to pay through the toll payment.
Muhuri's communication officer Ernest Cornel said those with no Safaricom lines are barred from using the ferry.
"Because they cannot pay through M-Pesa. They have cash, but they cannot pay. That is illegal!" he said.
Muhuri has already instructed their lawyers to draft a petition which they will present in court.
"If someone has cash, they should be allowed to pay and cross. We are moving to court to force them to stop using Mpesa payment only," he added.
In December, Muhuri chair Khalifa wrote the KFS demanding explanation of why users are being forced to pay their tolls using M-Pesa only.
They threatened to move to court should the decision not be reversed.