Officials in the country say these players now want asylum there.
The players were detained by police after refusing to board their flight repatriate propitious.
Suspected of refusing to return home even after trying influenced by Eritrea's ambassador in Botswana.
Eritrea was won 3-1 in the match for Botswana and ikabanduliwa from this race to qualify for the World Cup since it was imelazwa 2-0 in Asmara first leg.
Eritrean players have been disappearing frequently and refusing to return home.
Very kinachokumbukwa story is that of 2013, when Uganda ilipowapa 13 Eritrean asylum players and their team doctor after refusing to return home after playing the match.
Chief executive officer of the Botswana Football Federation has said it is still unclear is why the players refused to leave with their peers.
However, reports in Botswana newspaper The Voice says the players are afraid of being forced to join the army they return home.
In addition, it is claimed now they fear they may be charged with treason if they agree to return home.
The newspaper quoted the vice president of the Botswana Football Confederation discovered Basadi Akoonyatse saying the players were not at their rooms at the hotel Wednesday morning.
"The police were informed and after they searched tapikana roam around in the city of Francistown, claiming they were looking for the center of the Red Cross asking for help ... to get asylum in Botswana," he said.
Representative Dick Bayford players told news agency Reuters that he received information about efforts to remove these players from Botswana to power.

Eritrea has been accused for violation of human rights.
The report of the commission of inquiry of the United Nations, said the nation have cases of people tortured and enslaved.
The country has been accused by the UN by forcing citizens to join the army and kill people trying to flee abroad.
The Government of Eritrea imepuuzilia away, saying UN allegations are unfounded.