The exchange-traded fund (ETF) is run by celebrated financier and Pimco co-founder Bill Gross, who has been interviewed by US authorities, according to the Wall Street Journal.
The Pimco Total Return ETF has grown rapidly in the past couple of years.
Pimco said the investigation was a "private matter" and that its pricing procedures were "entirely appropriate".
The Californian firm confirmed it had been co-operating with the US regulator, the Securities and Exchange Commission (SEC), but did not elaborate on the nature of the investigation.
The Wall Street Journal reported on Tuesday that the investigation had been going on for months and concerned the manner in which Pimco purchased and valued certain bonds.
The company, widely considered to be the world's biggest bond manager, was set up in 1971, and acquired by insurance giant Allianz in 2000.
Shares in Allianz have fallen slightly following news of the SEC investigation.
A fund run by investment firm Pimco is being investigated over allegations that managers inflated returns.