"There is a new a provision that the passenger needs to have some sort of 'OK to Board' clearance from his ultimate destination," Bangladesh Cricket Board chief executive officer Nizamuddin Chowdhury said after Rubel, 27, was refused a boarding pass at Dhaka airport on Saturday.
"We are in touch with Cricket South Africa and hopefully the matter will be resolved soon. He will fly to South Africa on the first available flight once the matter is resolved," he said.
The rest of the 14-member Bangladesh squad has already arrived in South Africa ahead of the first Test starting at Potchefstroom on September 28.
The second and final Test will be played in Bloemfontein staring on October 6.
Rubel is now likely to miss the team's three-day warm-up match at Benoni near Johannesburg which begins on Thursday.
Chowdhury claimed Rubel's immigration clearance had nothing to do with a previous criminal allegation against the fast bowler.
In 2014, Rubel's former girlfriend and former actress Naznin Akter Happy had made a rape allegation against him, prompting police to detain him for several days.
A Dhaka court in May 2015 rejected the rape case against Rubel after police said there was no evidence against the bowler.
"I don't think it is the reason for him not to get the immigration clearance," said Chowdhury.
"His name is very common. Maybe someone else with the same name has some problem which created this problem," he said.
Rubel has taken 32 wickets from 24 Tests with one five-wicket haul.
Bangladesh will also play three one-day internationals and two Twenty20s during their month-long tour, their first to South Africa since 2008.
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First Published: September 19, 2017, 1:59 PM IST