Cricket South Africa said Boucher would have to attend a hearing Friday on five counts of breaching the body's rules and code of conduct following comments attributed to him in a newspaper article.
Boucher was quoted by the Business Day newspaper as suggesting there were ulterior motives for Kallis being out. "It is either those who have an issue with him, and have a chip on their shoulders, or those who have ulterior motives." He did not elaborate.
Boucher said of Kallis, who resigned as South African vice-captain after being out: "He's the best all-rounder we've ever had and he's saved more (limited overs) games than anyone realises - and he is a far better one-day player than he is given credit for."
He poured scorn on recent allegations about excessive drinking in the camp and the existence of a senior players' clique.
"In my off-season I have been doing some building on my house and reading about my being an alcoholic," he said. "I see pictures of myself and Herschelle (Gibbs) sitting at a pool-side bar and the accompanying article talks about how drinking is out of hand. It's all ridiculous."
Boucher, 30, a veteran of 102 Tests and 250 one-day internationals, was unapologetic about reports of a clique of senior players.
"Who do we want running things, the senior players or the junior players?" he asked. "When I first started out and I would see Hansie Cronje, Brian McMillan, Allan Donald, Gary Kirsten and Jonty Rhodes chatting together, I would simply think 'Oh, the senior guys are having a chat. That's fine. It's a good sign if the guys are getting together to discuss things - five heads are better than one'."
Unlike Kallis, his close friend and business partner, Boucher was picked in the Twenty20 squad but he was lukewarm about the tournament, to be staged in South Africa next month.
"First prize for those of us who love cricket is to be Test world champions. Second prize is to be 50-over world champions. Twenty20 only comes after those, really," he said.
Cricket SA announced Boucher would be charged under clauses relating to "unbecoming or detrimental conduct", making comments detrimental to the game, to a particular tournament or match, and critical of the selection of a team.