The committee voted 10-6 with three abstentions on Thursday to deny CPJ's application first made in 2012.
CPJ's application for consultative status was deferred seven times for procedural reasons before coming up for a vote at the request of the United States.
Human rights groups have criticized the UN's non-governmental organization committee for increasingly rejecting organizations for political reasons.
In a statement, CPJ called the application process "Kafkaesque" and blamed "a small group of countries with poor press freedom records" for employing bureaucratic delaying tactics. CPJ can still appeal the decision.