The list of firms to be investigated includes Aduno Holding, Postfinance, Swisscard and Swiss units of Credit Suisse and UBS, WEKO said.
The competition watchdog also added that raids were carried out at offices of the companies being investigated.
"We are surprised about this investigation and are convinced that the allegations will prove to be unfounded," Credit Suisse said in a statement.
"We already offer to consumers in Switzerland access to Apple Pay and Samsung Pay through our subsidiary Swisscard, of which Credit Suisse owns 50%. In addition, we have been in talks with companies such as Apple, Samsung or Google for several months to discuss how their mobile payment solutions could be offered to our clients."
A spokesperson for Credit Suisse also told CNBC Thursday that they will continue to work with Twint - a Swiss mobile payment app.
"Credit Suisse is very satisfied with Twint. The bank will continue to work very closely with Twint."
Local media reports suggest that the investigation is aimed at clarifying whether several Swiss financial institutions have reached an agreement to boycott mobile payment solutions from international providers such as Apple pay and Samsung. Authorities suspect that these institutions have jointly agreed not to release their credit card details for use with Apple Pay and Samsung Pay in favor of Twint.
UBS, however, said on Thursday that they were unable to reach agreement with Apple Pay despite having offered several alternatives.
"We do not comment on ongoing investigations, but would like to point out that in 2016 we tried to reach an agreement with Apple Pay regarding the use of UBS credit cards. Although we have offered several alternatives, unfortunately no agreement could be reached," UBS said in a statement.