Granted approval by the ACC to notify clubs, the NRL said it was not in a position to name the clubs or indicate how many are involved in Project Aperio.
The ACC last week released a report alleging the widespread use of banned substances in Australian sport, and possible links to organised crime and match-fixing.
The NRL said Monday's contact with clubs did not contain any specific details regarding the investigation.
"The information that has been passed on to the clubs is simply that they have been referred to within the report," NRL chief executive Dave Smith said.
"The NRL is working with the Australian Sports Anti-Doping Authority (ASADA) who will establish a more detailed briefing with the clubs regarding its investigation.
"The NRL does not have authority to name the clubs or confirm the number referred to in the report.
"Regardless of the outcome of any investigation, we are already committed to establishing the strongest integrity and compliance unit of any code and we are determined to see rugby league stronger for having addressed these issues."
The Nine Network on Monday claimed Curtis Johnston, a lower grader with NRL club South Sydney, had been stood down as part of an investigation into allegations he used performance-enhancing drugs.
Johnston, who plays for the South Sydney's NSW Cup feeder club North Sydney and has yet to play in the NRL, is reportedly at the centre of an investigation following a series of damning text messages.
It is not yet clear if the drama surrounding Johnston is linked to the ACC's report.
The Nine Network claimed it had secured possession of a series of text messages from Johnston boasting about his use of banned substances.
It is believed Johnston claimed the text messages were a joke.
While refusing to name the player or club involved, NSWRL boss Geoff Carr said a player had been stood down following an allegation of illicit drug use.
"There's been an allegation and the club has been cautious and stood the player down," Carr said.
"There has been no positive test."