Kenyan ch ampions Tusker FC and two Tanzanian sides Simba and defending champions Young Africans ind icated last week that they had pulled out because they are concerned about security in the host states of Durfur and South Kordofan.
Cecafa secretary general Nicholas Musonye told BBC Sport that Uganda Revenue Authority , wh o represented Uganda in the Champions League this year and finished runners-up in their domestic league, Ra yon Sport of Rwanda and Elect Sport of Chad will replace the teams that pulled out.
Musonye also reiterated his belief that the 18 June to 2 July tournament will be completely safe.
"We have made trips to Darfur and South Kordofan and the security is okay. There is no need for someone to sit in Nairobi or Dar es Salaam and imagine the security is bad.
"This is a very big tournament and we tried to convince the Kenyan team and the Tanzanian government that the security in these places is okay but they refused to believe us."
Musonye added that some changes will be made in the groupings when the Cecafa members and hosts Sudan Football Federation meet in Khartoum this weekend.
The championship, which is partly sponsored by the Rwanda President Paul Kagame, will now feature:
Al Ahly Shandi (Sudan), Al Nasir (South Sudan), Al-Hilal Kadugli (Sudan), Express FC (Uganda), URA FC (Uganda), Ports FC (Djibouti), Vital'O (Burundi), Merriekh El Fasher (Sudan), APR (Rwanda), Elman (Somalia), Rayon Sport (Rwanda) and Elect Sport (Chad).