The party's statement comes in the wake of reports of Chief Ministers of northeastern states recently expressing fears that the Centre would discontinue the region's special category status which assures them of financial support from Central Government.
The support, which is to the tune of 10 per cent of total Union budgetary allocation, is extended to states with economic and infrastructure deficiencies.
"Modi Government is moving towards a unitary form of government that is completely violative of the federal structure in our Constitutional scheme of things.
Yechury further accused the Centre of making "unilateral" appointment of "known" political workers as Governor of states including Tripura - where the communist outfit is in power.
He expressed concerns about alleged pro-Hindutva comments made by Tripura Governor Tathagata Roy.
"The recently appointed Governor of the Left-ruled state of Tripura has publicly spoken of his support to the hardcore Hindutva agenda being pursued by this Modi government. Such comments do not behove persons occupying such constitutional positions," he said.