The SNP National Council has traditionally been the body which sets party policy and acts as a bridge between members and the leadership.
A motion calling for its abolition has been submitted to the Aberdeen conference, though it has been opposed by a number of local branches.
The motion proposes a regional structure for National Assemblies in each of the eight Scottish Parliament regions with an expanded National Executive Committee, the party’s main leadership body.
Last night there was concern from some activists that the change could damage the party’s internal democracy and that the new structure would centralise more power at the top.
One leading activist said: “The National Council has been part of the democratic process of the party for a long time. It allows branches to put forward policy recommendations.”
The two-day party conference in the Aberdeen Exhibition and Conference Centre begins tomorrow and will end with a keynote speech from First Minister Nicola Sturgeon on Saturday afternoon.
Deputy First Minister and Education Secretary John Swinney will make the headline speech on the opening day.
Saturday will also see an appearance by Professor Clara Ponsati, the Catalan politician and academic who is facing extradition.
She will be joined by Aamer Anwar, her lawyer, and Joanna Cherry QC MP at the fringe event organised by Young Scots for Independence.
Prof Ponsati is a St Andrews University academic whose fight against extradition to Spain has become a cause celebre.