"This is an attempt to block the agreement which has been reached by the Transitional Military Council and the Alliance for Freedom and Change," General Jamal Omar of the ruling military council said in a statement broadcast live on state television, referring to the leading protest coalition.
Omar blamed soldiers from the army and intelligence officers, some of whom are retired, for carrying out the coup.
"The regular forces were able to foil the attempt," he said, without specifying when the alleged attempt was made.
Omar said of the 12 officers arrested, five of them were retired, and that security forces were looking for the mastermind.
The alleged coup comes as the ruling military council and protest movement leaders pursue discussions on a power-sharing deal with Ethiopian and African Union mediators.
Resisting protesters' demands
The landmark agreement reached last week, aims to form a new joint transitional civilian-military ruling body and is the first step toward installing an overall transitional civilian administration in Sudan as demanded by demonstrators.
On Thursday, the ruling military council was due to hand over a draft document on the establishment of the interim government, to rule for three-years before elections are held.
Sudan has been rocked by a political crisis since protests first erupted against Omar al-Bashir's nearly 30-year rule in December.
The protests finally led to the army ousting him on 11 April, but the generals who seized power have so far resisted demonstrators' demands to hand the countryover to a civilian administration.