Retiring ex-skipper Shakib Al Hasan told local media Thursday he was not returning to Bangladesh because of "a security issue", potentially missing what he says will be his final match for his country.
Asif Mahmud, who heads the sports ministry, said he had advised the cricket board to discourage Shakib from returning because of public anger.
As well as a cricket star, Shakib is an ex-lawmaker in the government ousted by a revolution in August.
The 37-year-old announced his retirement from international cricket last month but said that he wanted to play one last Test series at home.
He was named in the Bangladesh squad to face South Africa, with the first of two Tests starting October 21, and had been expected to fly back to Dhaka on Thursday.
Shakib is a former lawmaker from the party of autocratic ex-leader Sheikh Hasina, who fled by helicopter to India in August.
He is among dozens from Hasina's party facing murder investigations for a deadly police crackdown on protesters during the uprising.
"I was to return home... but now I don't think I can," Shakib told broadcaster bdnews24.com.
"It is over a security issue, a matter of my own security."
Shakib apologised in a Facebook post earlier this month for remaining silent during the revolution.
But Mahmud, from the interim government's cabinet, said that "recent protests suggest it wasn't enough" and that to avoid "unwanted incidents" he had advised Shakib not to return.
"This decision was made to ensure the safety of players and to protect the country's image," Mahmud said in a statement.
Bangladeshi media said Shakib was in Dubai but would be heading to the United States.
Shakib was playing in a domestic Twenty20 cricket competition in Canada when the regime collapsed and has not returned to Bangladesh since. He toured Pakistan and India with the Bangladesh team.
The first Test against South Africa in Mirpur, near the capital Dhaka, will be the first international cricket fixture in Bangladesh since crowds stormed Hasina's palace.
More than 700 people were killed in the unrest, according to Bangladesh's health ministry.
The second Test will be played in the port city of Chittagong, also called Chattogram, beginning October 29.
Hasina's 15-year rule saw widespread human rights abuses, including the mass detention and extrajudicial killings of her political opponents.
Earlier on Thursday, a court in Bangladesh issued an arrest warrant for Hasina to face charges, including crimes against humanity.