Two-time Tour de France champion Alberto Contador's Saxo-Tinkoff team was granted an automatic spot for the top events of 2013, at the expense of world No.1 Joaquim Rodriguez's Katusha team.
"The request from the team Katusha for registration in the first division has been rejected," the International Cycling Union (UCI) said in a statement without elaborating.
"In accordance with UCI regulations, this team’s application has been forwarded to the UCI administration, so that the latter may assess the possibility of registering this team as a UCI Professional Continental Team."
UCI spokesman Enrico Carpani told Reuters that the decision had been taken by the independent Licence Commission, which makes its decisions on sporting, ethical, administrative and financial grounds.
Katusha was on the list of the top 15 teams by sporting value so was rejected for other reasons.
The status of Contador's team was under threat because Saxo-Tinkoff finished outside the top 15 in 2012. Its licence now extends to the end of 2014.
The decision means that Katusha, which finished second in the WorldTour standings in 2012, will need invitations to take part in the Tour de France, the Giro d'Italia, the Vuelta a Espana and several top one-day and one-week races.
Rodriguez, 33, claimed victory in the Fleche Wallonne classic as well as the Giro di Lombardia this year.
The Spaniard also finished second at the Giro d'Italia and third in the Vuelta a Espana as he claimed top spot in the year-end WorldTour standings.
Russian Denis Menchov, a two-time winner of the Vuelta and 2009 Giro champion whose name was mentioned in connection with disgraced trainer Michele Ferrari in October, is another notable member of the Katusha team.
Pro Continental outfit Argos-Shimano was a big winner in the process with the UCI graduating the team to WorldTour status for the next four years.
“This World Tour licence is a reward for the combination of a strong group of riders and innovative coaching staff, who have managed to get into the World Tour through their own efforts," said General Manager Iwan Spekenbrink.
"It’s greatly satisfying to work with a team that’s growing mainly through developing itself. The granting of this licence is also certainly what our faithful sponsors deserve."
Nine teams with current UCI licenses including Orica-GreenEDGE, Astana, BMC, Cannondale, Lampre-Merida, Omega Pharma-QuickStep, Sky, Vacansoleil-DCM and Movistar had their places green-lighted in early November.
Further hearings awarded extended WorldTour licences to AG2R-La Mondiale (2013-2016), Euskaltel Euskadi (2013-2016), Former Rabobank (2013-2014) and Garmin-Sharp (2013-2014) The Licences Commission also granted single season registration to FDJ, RadioShackNissan and Lotto-Belisol.
"That we can ride all WorldTour races is reassuring," said Lotto Belisol general manager Marc Sergeant. "For all riders, staff and sponsors this is excellent news. It is also good for Belgian cycling, it was almost unthinkable that Lotto Belisol wouldn’t have got a licence."
The UCI said the full list of Professional Continental Teams registered for 2013 will be announced at a later date.
UCI WorldTour teams for 2013
AG2R La Mondiale