A long-time critic of City, Tebas stated at the FT Business of Football Summit that the complaint was lodged in 2023.
He added that the case is now in the “investigation phase” under the European Commission, which oversees and enforces laws across the EU.
Tebas said: "City have a lot of companies in their group which lie outside the City Football Group structure, extra companies where they put their expenses.
"These other companies lose the money but not the club itself. We have reported Manchester City to the EU. We have the facts and figures.
"We asked for City to be checked. It's very important that all clubs are subject to the same transparency rules and governance on both the sporting and financial side.
"The City case is one where we believe they have put the losses on the companies that are not officially part of City Football Group."
He added: "They have a scouting company, a marketing company. That's where they have very high expenses. They invoice City for less money.
"City have costs that are less than if they didn't have this circle of companies around."