The broadcaster managed 26 award nominations, substantially fewer than those of rival channels CBS (60), NBC (51) and ABC (48).
"Seminal shows like House and 24 have cycled out," Reilly told reporters at the Television Critics Association Press Tour. "Next year we will have some [more]."
The 2012 Emmy nominations for 'Best Drama' are comprised entirely of cable shows - including Homeland and Game of Thrones - with no recognition for network series.
However, Reilly argued: "Cable hits would not make it in a network universe."
The network head later named Kiefer Sutherland's Touch and Fox's new shows - which include Kevin Bacon's The Following and The Mob Doctor - as potential Emmy candidates for 2013.
> Homeland, Downton, Breaking Bad: Which show should win the Drama Emmy?
> Homeland, Sherlock: Tube Talk on the Emmy 2012 nominations
Watch a trailer for Fox's new drama The Following below: