The company received a "Wells notice" from the agency over the fund, which was once managed by Bill Gross. It is neither a formal allegation of wrongdoing nor a finding that a law was violated.
Read MoreWells Notice—CNBC Explains
The SEC may recommend civil action against Pimco related to the value of smaller positions in nonagency mortgage-backed securities the fund bought in 2012. A nonpublic investigation also looked into the fund's performance disclosures as well as compliance policies.
"The Wells process provides us with our opportunity to demonstrate to the SEC staff why we believe our conduct was appropriate, in keeping with industry standards, and that no action should be taken. We will continue to engage with the SEC and we are confident that this matter will not affect our ability to serve our clients," Pimco said in a statement Monday.
Gross left Pimco last year and now works at Janus Capital.
—Reuters contributed to this report