Kitutu Masaba Clive Gisairo claimed that the new method was just a way for the government to bring more systems into the Kenya Revenue Authority system.
Mr Gisairo dismissed the system, saying it would make life harder for parents, especially those struggling to make ends meet.
'How will this system work? Will parents who pay school fees through cows and goats be forced to go to the cyber cafe and make their payments there?' asked Mr Gisairo.
Mr Bitok was invited by the committee to give an update on the implementation of the presidential directive on payment of school fees through the eCitizen platform.
Mr Bitok was also asked to outline the challenges faced in implementing the directive and the measures taken to mitigate them.
While defending the payment system, Mr Bitok said it will help parents who have suffered at the hands of school principals who charge fees not approved by the Ministry of Education.
'Some head teachers have been charging fees that are not approved by the government. This has been going on for some time. Through this system, there will be no such fees and parents will only pay what has been approved by the Ministry of Education,' Mr Bitok said.
He also told the MPs that the Ministry of ICT has already started connecting most schools in rural areas to the internet to facilitate seamless payment of fees.
On the Sh50 that parents will be charged upon payment, Mr Bitok told MPs that the government has already reached an agreement with Safaricom to remove the fee.
'The payment will be free, we have agreed with the service provider, which is Safaricom, that they should not charge the Sh50 as is the case with other government services,' Mr Bitok said.
The High Court is expected to hear today a case filed by Nakuru-based surgeon Dr Magare Gikenyi challenging the directive on the payment method.
The High Court has temporarily suspended plans for parents to pay their children's school fees through the eCitizen platform.
On January 31, Education PS Belio Kipsang wrote a circular to all head teachers stating that all parents must pay school fees through the eCitizen platform.
Earlier, Cabinet Secretary for Treasury (CS) Njuguna Ndung'u announced a Sh50 fee for every transaction made on eCitizen.
