Scientific museums in the Russian Federation, in accordance with current legislation, are switching to the collection management standard developed for the Ministry of Culture. The absolute priority of preserving museum items is a serious obstacle to the implementation of the standard, which greatly limits the possibility of their scientific examination, which is contrary to the interests of scientists. The examination of museum items, like any other use, including exhibiting, inevitably has a negative impact on their preservation. At the same time, the examination serves to increase the value of any item, its relevance for modern culture. The methodology of scientists’ work with collections began to form in the period of antiquity. In our country, tools for processing, describing, systematizing and storing collections were formed in the 18th–19th centuries, namely in scientific museums, museums of the Academy of Sciences. Museums in the Russian Empire were part of the scientific organization system. However, after the Soviet reforms in the 1930s, museum and scientific activities were radically separated. As a result, the research function of museums under the Ministry of Culture is poorly implemented, which is enshrined in current regulatory documents. Scientific museums, due to their subordination to the Ministry of Science and Higher Education, have scientific research as their target indicators, which determines their priority over traditional museum indicators (storage and replenishment of funds, exhibits and attracting visitors). Attempts to combine the interests of examining and preserving collections have been discussed for several decades. This problem is especially evident in relation to natural science collections and museums, most of which are under the scientific department. Its solution requires the development of a methodology for handling museum collections and amendments to regulatory documentation.