Smith was speaking after it was announced that ICC appeals commissioner Richie Benaud had rejected Gibbs' appeal against a ban imposed by match referee Chris Broad for remarks picked up by stump microphones during the first Test in Centurion.
Gibbs will miss the third and final Test against Pakistan starting at Newlands Friday, as well as a Twenty20 international and the first One-day international against Pakistan next month.
Asked for his reaction, Smith told his captain's pre-match press conference: "It's a tough one. It is disappointing. We have one or two gripes with the ICC, I guess, and maybe this is not the forum to discuss it.
"Maybe we need to get on the phone with (cricket general manager) Dave Richardson and (chief executive) Malcolm Speed and discuss these things.
"We are disappointed at losing Herschelle. We just want to see consistency in decision making around the world. We've experienced things that haven't been dealt with."
Smith was believed to be referring to incidents that involved the South African team in Australia last season in which it was alleged racist remarks had been made against the South African players.
An official Cricket South Africa response was being formulated, according to media manager Gordon Templeton, but he said CSA were pleased that Benaud said he did not believe that the remarks made by Gibbs meant that the player was a racist.
In the ICC statement, Benaud said: "At Chris Broad's hearing (Pakistan team manager) Talat Ali spoke about the offence the words used by Herschelle would give to the whole Pakistan nation. I am not surprised.
"(However), as an Appeals Commissioner and a person, I certainly do not consider Herschelle to be a racist and I take great exception to the suggestion, in the same way I believe Chris Broad would object (to suggestions his finding would do the same)."
While Smith was critical of the ICC, he appeared to have softened his stance on stump microphones after saying after the initial hearing against Gibbs that he believed television companies were to blame for leaving the microphones on instead of switching them off immediately after a ball had been bowled.
Smith said Thursday: "Stump mikes are there. They're part and parcel of the game. You can't even talk at third man now. There's a part of me that would like them to be turned down but there's a part of me that realises cricket is a sport that's got to compete with other sports around the world. I'm sure there are people around the world who want to hear what's going on.
"Players are in a sort of 50-50 situation where they would like it to be more private but they also realise that cricket's got to move with the rest of the world."
Benaud upheld Broad's finding that Gibbs was guilty of a Level 3 offence under a clause which prohibits using "any language or gestures that offends, insults, humiliates, intimidates, threatens, disparages or vilifies another person on the basis of that person's race, religion, colour, descent or national or ethic origin."
Gibbs' remarks were in reaction to abusive spectators. According to Cricket SA chief executive Gerald Majola and newspaper reports the words allegedly used by Gibbs included "these fxxx Pakistani animals", a reference to "fxxx baboons" and a suggestion that the spectators should "fxxx off back to Pakistan".
In his findings, Benaud expressed surprise that the behaviour of the spectators had not been drawn to the attention of match officials and had only been reported to security personnel.
Although the ban was originally for two Tests, it was changed to one Test and two one-day games in terms of the ICC code which specifies that bans should apply to the next matches in which a cricketer is due to play, with two One-day games being the equivalent of one Test match.
Gibbs will be replaced by Boeta Dippenaar for Friday's Test. Also missing will be all-rounder Shaun Pollock and fast bowler Andre Nel, who are being rested. They will be replaced by Andrew Hall and Dale Steyn.