The foreign minister is part of a nine member delegation headed by the deputy prime minister Osman Jamal Ali which arrived in the Ethiopian capital on Wednesday with the aim of bolstering weakening diplomatic relations between the two countries.
Somalia's interim government has admitted that it was wrong to accuse Ethiopia of meddling in Somalia's internal affairs.
The unprecedented move follows months of accusations that neighbouring Ethiopia has been launching cross border attacks into the south-west of the country, and actively supporting Somali warlords with the intent of undermining the Mogadishu government.
Somalia's foreign minister, Ismael Hurreh Bubah told the BBC in Addis Ababa that the accusations were based on "exaggerated information".
"I think that some of assumptions and assertions were based on wrong information. I don't see why Ethiopia would send troops across the border into Somalia. I believe there are no Ethiopian troops out there and Ethiopia has assured us of that. The transitional national government (TNG) believes Ethiopia is committed to the peace and stability of Somalia", said Mr Bubah.
Mud-slinging past
"I have to be honest, things between our two governments have not been smooth. There was some mud-slinging in past, but now we are coming round to reality and we have to sit together and discuss these matters and see the best way to move forward," he added.
The foreign minister is part of a nine member delegation headed by the deputy prime minister Osman Jamal Ali which arrived in the Ethiopian capital on Wednesday with the aim of bolstering weakening diplomatic relations between the two countries.
They first held talks in November last year, but since then relations have become increasingly strained.
Somali Prime Minister Ali Khalif Galayr has on numerous occasions accused Ethiopia of arming factions opposed to the government, occupying Somali districts and increasing its military presence in the country.
Ethiopia has responded by saying the TNG was using Ethiopia as a scapegoat to divert criticism away from its inability to control the country.
Warlords
Addis Ababa has also hosted talks between the Somali faction leaders opposed to the TNG, who set up the Somali Reconciliation and Restoration Council (SRRC), to work towards what they described as a "legitimate" and "more representative" government in Somalia.
The Foreign Minister said that the TNG did not oppose Ethiopia's
intervention with those faction leaders.
"Ethiopia is open to everyone. Many Somalis come into Addis Ababa and discuss matters with the Ethiopians. The SRRC are part of that. We are not adverse to Ethiopia carrying out discussions with them as it's all part of the reconciliation and peace process," said Mr Bubah.
"We believe Ethiopia is working to bring about a peaceful and stable Somalia," he added.
Talks between the two governments, which have been described by both parties as "cordial and procutive" are expected to conclude on Friday.
Sources say that discussions focused on how to move forward the reconciliation process in Somalia as well as border security.
Sources say Ethiopia has re-iterated its position that Somalia should have a broad-based government incorporating all factions.
The Somali delegation are expected to return to Mogadishu on Saturday.