Director Press and Public Relations in the ministry, Mohammed Manga, made the disclosure in a statement issued in Abuja.
The federations were being run by caretaker committees since their dissolution in April by Minister of Youth and Sports Development, Sunday Dare.
The minister had promised to ensure credible elections into the federations after the Tokyo Olympics and the Paralympic Games in September.
Manga said that the six national sports federations that had had their constitutions ratified by their international sports bodies and the Nigeria Olympic Committee (NOC) would conduct their elections based on their respective constitutions.
He said that the ministry had also directed that the federations should begin all necessary process, as outlined in their constitutions towards having elective congresses on September 30 in Abuja.
The director listed the sports federations expected to hold elections to include: Nigeria Aquatics Federation, Nigeria Basketball Federation, Nigeria Boxing Federation, Cycling Federation of Nigeria, Nigeria Shooting Federation as well as Nigeria Table Tennis Federation.
He, however, stated that other sports federations, which had yet to ratify their constitutions, would also conduct their elections on same day with the guidelines provided by the ministry.
According to Manga, the ministry and the NOC will serve as observers in all the elections.
He called on Nigerians and stakeholders, with interest and passion for their identified sports, to feel free to get involved with the process of elections, in line with democratic principles.