NASA co-principals Kalonzo Musyoka, Moses Wetangula and Musalia Mudavadi's parties' are not entitled to claim a share from Raila Odinga's ODM.
The Orange Democratic Movement party was awarded Sh4.1 billion after years of court battle, which is an equitable share for strengthening of political parties.
For the last two elections, Ford Kenya, Amani National Congress and Wiper parties have either closely worked with ODM or supported Raila Odinga's presidential bid.
But Registrar of Political Parties Ann Nderitu on Thursday said the 2017 pact did not mention anywhere that ODM would share the funds with the other parties.
The document, according to Ms Nderitu, only contained how the four partners would have shared power if they formed the government.
“When dealing with coalitions, we go by what the parties agreed in the MoU. If it gives a formula of sharing of funds, then we go with that,” said Nderitu.
She explained that in the event there is no such declaration, then they rely on the Political Parties Act, which stipulates the requirement for a political party to benefit from public funding.
“In this particular case, the MoU did not stipulate such a formula and, therefore, we cannot enforce the sharing of the funds. We go by what the Act provides,” she said.
The blow to the three comes at the time ODM is at loggerheads with Mudavadi over President Uhuru Kenyatta's pact with Raila Odinga, following the former VP's claims that the Handshake was brought about by pressure from the West.
Last week, ODM Secretary General Edwin Sifuna insisted that the coalition is dead, a claim which was backed by former Machakos Senator Johnstone Muthama.