The party chairman and senior leader Johnny Nellore termed the decision as a "brutal cheat".
UDF Convener P P Thankachan has formally informed Nellore the Kerala Congress (Jacob) should be satisfied with just one seat, Piravom, currently represented by Food Minister and party leader Anoop Jacob.
The party had contested three seats in the 2011 Assembly polls.
It could be possible due to hard bargaining the late party leader T M Jacob did with the Congress leadership. Nellore had contested from the Angamaly seat.
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Nellore said the party has no untouchability towards the CPI(M)-led Left Democratic Front and the BJP-led NDA.
He said the party's leadership will meet this evening to discuss further course of action.
Meanwhile, Anoop Jacob said he would comment on the issue only after the party's meeting this evening.