A bench headed by Justice A K Patnaik dismissed the plea of former Maharashtra chief minister Ashok Chavan challenging the Commission's jurisdiction to enquire into such issues.
It directed the Commission to enquire into the complaint against Chavan within 45 days.
The apex court passed the order on an appeal filed by Chavan challenging the Delhi High Court verdict which had refused to grant any relief to Chavan on the issue of paid news.
The probe was launched by EC on the complaints filed by BJP leaders Mukhtar Abbas Naqvi and Kirit Somaiyya.