Ali Bacher, the managing director of the United Cricket Board of South Africa, said that he had been told by Steve Camacho, his West Indian counterpart, that Lara, the vice-captain Carl Hooper, and the senior player Jimmy Adams, had all failed to arrive.
The three players are believed to be in London with six other members of the 16-man squad selected for the five-Test tour.
Seven players, plus the manager, Clive Lloyd, and the coach, Malcolm Marshall, arrived in Johannesburg yesterday, with the whereabouts of the pace bowlers Courtney Walsh and Curtly Ambrose a mystery.
According to Bacher, the players were represented in Antigua by two members of the recently formed West Indian players association, the former Test players David Holford and Roland Holder.
Lara was appointed captain last year and led the West Indies to a series win over England, but he has had several clashes with officials.
Lloyd, meanwhile, is determined to bring a cricketing element back to the tour. The seven players in South Africa will have a net practice at the Wanderers ground in Johannesburg today. Yesterday, though, Lloyd cancelled a scheduled press conference, saying he would wait for the outcome of the meeting in Antigua before making any statements.
Lloyd said the fate of the tour lay in the hands of the West Indies Cricket Board, which is embroiled in tense pay-for-play negotiations in Antigua with Lara and Hooper.
"Everything is dependent on the outcome of the talks," said Lloyd, who added he had been aware of meetings taking place during the Wills International Trophy knock-out tournament in Bangladesh last month, but since then had not been in contact with Lara.
"Whether the tour goes on, with or without Lara, would be entirely up to the West Indies Board," Lloyd said.