It emerged last week that Carter was one of three Racing players who tested positive for corticosteroids prior to last season's Top 14 final.
The fly-half has failed to recover from a calf injury sustained last month.
Wing Joe Rokocoko and fellow back Juan Imhoff, the other players to test positive, are both in the Racing team for Sunday's game.
The trio were interviewed on Wednesday by French Rugby anti-doping chiefs, who will decide whether the players and Racing have broken any rules.
Racing said the players did not have therapeutic use exemptions (TUEs) for "anomalous" drugs tests but insist the players have not done wrong.
Carter and Rokocoko scored 20 of Racing's points in the 29-21 Top 14 final win over Toulon last June.
With Carter missing a third straight game, South African Johannes Goosen will start at number 10, fresh from turning out for the Springboks in the Rugby Championship.
Centre Henry Chavancy returns for last season's beaten European finalists with Camille Chat replacing injured skipper Dimitri Szarzewski at hooker.
Other big names in the Racing team include France internationals Eddy Ben Arous and Maxime Machenaud, who captains the team, plus ex-Glasgow star Leone Nakarawa.
Munster make only one change from last weekend's Pro12 defeat by Leinster with Jaco Taute replacing injured Keith Earls at centre.
Ireland international Earls is following return to play protocols after picking up a knock last weekend.
Fly-half Tyler Bleyendaal and wing Darren Sweetnam will both make their European debuts for the Irish province.
TEAMS
Racing 92: B Dulin; J Rokocoko, H Chavancy, A Tuitavke, J Imhoff; J Goosen, M Machenaud; E Ben Arous, C Chat, B Tameifuna; L Nakarawa, M Carizza; W Lauret, Y Nyanga, C Masoe.
Replacements: V Lacombe, V Afatia, C Gomes Sa, F van der Merwe, T Dubarry, J Hart, R Tales, A Vulivuli.
Munster: S Zebo; D Sweetnam, J Taute, R Scannell, R O'Mahony; T Bleyendaal, C Murray; D Kilcoyne, N Scannell, J Ryan; D Ryan, B Holland; P O'Mahony (capt), T O'Donnell, CJ Stander.
Replacements: D Casey, B Scott, S Archer, R Copeland, J O'Donoghue, D Williams, I Keatley, D Goggin.
All Blacks great Dan Carter will miss Racing 92's European Champions Cup opener against Munster on Sunday.