The European Handball Federation (EHF) writes on its website that the Macedonian duo have submitted a "suspicious video" and have therefore been excluded.
Before the European Championship finals, referees must submit a video documenting their physical form eight and four weeks before the start of the tournament, respectively.
In the video, they complete a physical test that is then analyzed by fitness experts.
It is here that the EHF believes it has found signs of cheating.
"After receiving the recordings from Nikolov and Nachevski, the EHF became aware that the videos from the two referees may have been manipulated and may not show an accurate recording of the entire test," the federation writes on its website.
"The in-depth analysis showed that the videos have most likely been manipulated."
The European Handball Championship begins on Friday, with Sweden, Denmark and Norway hosting the tournament.
Sweden begins the European Championship against the Netherlands on January 17.
