Citing people close to the matter, the report said the Federal Trade Commission is asking firms to identify their largest shareholders and their influence over them.
The news adds to the growing scrutiny of the power the major ETF players have over the companies they own.
The huge flows have led the Big Three to become the largest owners of many US publicly traded firms.
Typically, the trio collectively own 22% of the S&P 500, according to Bloomberg data. This gives the companies significant influence over major decisions such as mergers.
This dominance has led to anticompetition criticism from academic circles. For example, José Azar, professor at IESE Business School, Universidad de Navarra, argued competition issues benefitted shareholders but impacted consumers and savers.
He found in a 2014 paper, aeroplane ticket prices were 3-7% higher "due to common ownership".
Meanwhile, Einer Elhauge, president of Legal Economics and petrie professor at Harvard Law, told ETF Stream last year investors would be impacted by horizontal shareholdings as, although it can increase profits, it can also create antitrust liability risk.
The new developments in the US represent another hurdle for companies looking for regulatory approval when merging.
The inquiry means investigators are now looking at the influence institutional investors have over the companies they hold majority stakes in.