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The paper reveals the issue of the scientific research efficiency, which is in the center of modern scientific and philosophical debates. This problem is interpreted as a contradiction between efficiency and autonomy – the two significant features of academic research. This contradiction became urgent in the second half of the 20th century and is expressed in the crisis of institutional interactions or a clash of interests between academia and its governing stakeholders. The paper provides a brief description of the historical prerequisites of this contradiction, obtains insights into the modern crisis and outlines possible ways out. As a conclusion, it emphasizes that the issue of academic efficiency may be solved through a new system of adequate representation of scientific research that would also act as a metric of academic efficiency, thus aligning the targets of various entities engaged in the academic activities. The crucial preconditions for this system in Russia are the formation of a consolidated academia and aligned targets of the academic policy.