Mohammad Esmat was part of a delegation holding talks with Abiy Ahmed, who flew in from Addis Ababa on Friday.
No further details were given about his arrest.
His visit follows the deaths of dozens of people when troops stormed a protest camp on Monday following long demonstrations against military rule.
Mr Ababa held discussions with both the Transitional Military Council (TMC), and the opposition Declaration of Freedom and Change Forces (DFCF) alliance.
As he tried to mediate, Mr Ahmed urged both sides to exercise “bravery” in resolving their standoff.
He arrived in Sudan the day after the African Union – based in Ethiopia – suspended Sudan, backing the opposition’s demand for civilian rule.
“The military and the people and the political forces need to act with bravery and responsibility in taking quick steps to a democratic, re-conciliatory transitional period in the country,” Mr Ahmed said in a statement.
His diplomatic skills have been praised after he negotiated peace with Ethiopia’s neighbour Eritrea.
Sudanese protesters blocking a street in Khartoum earlier this week
The TMC took over after Sudan’s long term ruler, Omar al Bashir, was overthrown by the military in April.
It is proposed that a sovereign council lead Sudan for three years as it embraces civilian rule.
But there has been persistent deadlock in talks between the protesters and the military.
The demonstrators want limited military representation on the sovereign council, but the generals want overall control during the interim period.
