Mr Mudavadi said that the meeting between Mr Odinga and Mr Kenyatta was not discussed through the Nasa structures.
"Indeed nowhere does the MoU allude to or mention Nasa, including the signing off. Instead, the two repeatedly invoked their names and personally committed to each other and not to all Kenyans," the ANC leader said.
He was in Mombasa for a meeting with ANC leaders.
Those in attendance included ANC national chairman Kelvin Lunani, Nambale MP Sakwa Bunyasi and his Sabatia counterpart Alfred Agoi.
On Friday morning, Mr Odinga and Mr Kenyatta met at Harambee House in Nairobi.
In a joint statement, they said they would work together in the best interest for Kenyans.
Some leaders and citizens praised them and described them as statesmen for putting aside their differences and putting Kenyans’ interests before their own.
However, others were sceptical of the agreement, while the three Nasa co-principals – Mr Mudavadi, Mr Kalonzo Musyoka of Wiper and Mr Moses Wetang’ula of Ford Kenya – said they were unaware of the discussions.