FIFA's executive committee agreed on Friday to allow teams from its member associations to play Kosovo sides at "youth, amateur, women's and club football" level.
However, it made no mention of Kosovo's request to play at senior international level.
"The FIFA executive committee decision is an important decision because it recognises Kosovo's role and participation in international football," said FFK president Fadil Vokkri in a statement sent to Reuters.
"We will make the best out of it for the good of our players, teams and clubs.
"But that decision is disappointing and not fully satisfactory because it seems to exclude the top national team for unexplained reasons."
Kosovo had not previously requested FIFA membership, but Vokkri said that had now changed.
"The FFK will present its request for affiliation to FIFA which is the logical step since the majority of the United Nations member states, 97, have recognised Kosovo," it said.
"One hundred and eighteen of FIFA's 209 member associations represent countries and territories having recognised Kosovo, meeting the criteria defined in... the FIFA statutes for the affiliation."
FIFA agreed in principle to allow Kosovo to play friendlies last May but, following opposition from Serbia and UEFA president Michel Platini, has dallied over how to implement the ruling.
In September, Albania captain Lorik Cana and Swiss internationals Xherdan Shaqiri, Granit Xhaka and Velon Behrami were among several Kosovo-born players who sent a declaration to FIFA backing the FFK's campaign.
Kosovo declared independence from Serbia in 2008 but has not yet won recognition from the United Nations.
On membership, FIFA statutes state: "Any association which is responsible for organising and supervising football in its country may become a member of FIFA. In this context, the expression "country" shall refer to an independent state recognised by the international community."
However, countries can only join FIFA if they are first members of a regional confederation and UEFA only accepts applications from countries which are recognized by the United Nations.