The minister met Sheikh Sharif Sheikh Ahmad and Sharif Hasan Sheikh Adan, who were given very tight security.
They discussed the political situation in Somalia, and how the opposition could dialogue with leaders of the Somali Transitional Federal Government.
Secret reports say the Yemeni foreign minister proposed to the opposition leaders that there be direct talks with Somali government leaders, by telephone, and that Yemen would facilitate the process.
Yemeni foreign affairs officials say the opposition leaders have accepted the idea of talking to Somali leaders, and would like to meet Somali government officials in Yemen.
Sheikh Sharif Sheikh Ahmad and Sharif Hasan Sheikh Adan are due to discuss the Somali crisis this evening with Yemeni President Ali Abdallah Salih.
No official reports on the meetings in Yemen have been made.
This comes as the Islamist leader Sheikh Hassan Dahir Aweys has declared that the organization is scheduling to replace Sheikh Sharif Sheikh Ahmed from the chairman of the group into another new leader although he rebuffed to mention the name of the successor.
In an interview with Al-Arabiya Arabic TV he declared that they were planning to take a decision on to strip sheikh Sharif from his post of the ARS.
"He sullied the laws of the group, so we cannot put up with him to include in our group" Aweys said.
Asked about the allegations from Sharif against Eritrean government saying that Eritrea has started to come apart the ARS group he stated that Eritrea played required role on the advancement of the group.
He also said that they will hammer out this issue at a consultation meeting they would hold in the upcoming days.
"That meeting will be resigned Sharif" Aweys 62 added.
He also acknowledged that there were failed mediation between him and Sheikh Sharif.