This paper focuses on the scientific activity represented through an organized network of publications. On the one hand, scientific publication refers to the autonomy of science community. On the other hand, research management takes it as an instrument of control and evaluation of science. The article aims at the determination of origin and resolving the contradiction associated with such ambiguity of scientific publication. The investigation proceeds from the conceptual grounds of modern epistemology and philosophy of science studying the crisis of scientific representation. The authors 1) explicate the concept of representation and its medial status, i.e. mediation between «who» represents and «what» is represented; 2) clarify the conditions under which the crisis of representation occurs: its medial status fails; representation becomes an obstacle to understanding the latter; 3) describe the possibility of overcoming the crisis, which consists in shifting attention to the conditions of producing representation. The medial status of representation of the scientific activity through publication has three levels: inter-scientific, reflexive and outer-scientific. Particular attention is paid to the third level. At this level, the publication activity serves as a medium between scientists and research managers. The authors of this paper diagnose the transformation of the publication from a medium of fruitful interaction between all actors interested in science to a resource of efficiency. That transformation creates obstacles for the development of science. The representation of science by means of scientometrics for managers surrogates the scientific activity itself. In the last part of the paper, specific strategies are described, which aim at restoring the medial status of representation of the scientific publication and determine the effective science policy.