The former grand final official takes over as the elite performance manager, following confirmation of Daniel Anderson's departure to the Parramatta Eels.
NRL head of football Todd Greenberg said Archer's interim appointment was pending a review of the refereeing structure after another controversial year for officials.
It continues the revolving door at NRL headquarters.
Veteran former ref Bill Harrigan was sacked after the 2012 season, and the NRL elected to move in a new direction by appointing an ex-coach in Anderson.
But after the World Cup concludes, Anderson will leave the high-pressure post after just one season in charge and return to clubland to head up the Eels' new-look football department, overseeing new coach Brad Arthur.
His departure means it's time for another review, with the NRL to look at another new model.
"There is no more important area in the game than officiating," Greenberg said.
"From the grass roots to the NRL there is a real need for people to appreciate and respect the importance of the role.
"Daniel has done a fine job in establishing a genuine high performance unit for the referees and he has left us a really solid foundation on which we can build.
"There are a number of options we could now look at in terms of a game-wide approach to refereeing and it is worth taking the time to form a long-term strategic view.
"Daniel will complete his commitments with the World Cup and Tony has agreed to the interim role during our review process.
"We are sorry to see Daniel leave and we thank him for what he has achieved but we also need to look at the chance to take what we have learnt this year and apply it to building an even stronger framework in the future."