Wa Mutharika had been negotiating with the Republican Party, a coalition of four minority parties, as well as the Movement for Democratic Change, but the groups said on Tuesday the talks were over.
"We cannot be swallowed by a party that does not have a manifesto or even a constitution ... We only indicated that we would work with government in supporting issues in the national interest," said Aleke Banda, leader of the Republican coalition.
The Movement for Democratic Change said it was reviewing its earlier commitment to support the government by taking all the issues to a party convention.
"We have to consult the people now before we make any commitments to either join the party or support government and the convention is the only way to do that," Chairman Greene Mwamondwe said.
The Republican representative at the talks, Aaron Sangala, said his party was still ready to work in a coalition but not to join a party under wa Mutharika's leadership.
The chairman of wa Mutharika's negotiating team, Paul Maulidi, the president's camp still hoped for a deal.
"Despite the fall out of the formation of one party, negotiations are still continuing and we are still hoping that the parties will have a change of heart since they pledged to serve the interests of government," Maulidi told.