The two companies serve around three-quarters of the Czech market and began cooperating in 2011 in an attempt to expand their rollout of 3G and 4G. It covers all of the Czech Republic except Prague and Brno.
Vodafone is the only other operator in the country, and is smaller than the others. It is not part of the network sharing deal.
The EC said it will look at how the agreement impacts quality improvements in existing infrastructure, and whether it causes delays to the deployment of new technologies or services.
If the investigation finds it is in breach of competition rules, O2 and the Deutsche Telekom subsidiary may have to end the arrangement, or modify it.
CETIN is an infrastructure firm that was span off from O2 Czech Republic last year when the company was split in to two. It runs the fixed-line access network, mobile access network and international services previously offered by O2 Czech Republic.
In a statement to Reuters, T-Mobile said: “We are closely cooperating with the European Commission in the given matter. We are convinced that cooperation in the area of network sharing does not curb competition nor innovations. On the contrary it brings benefits to end-customers."