Writing in his weblog, Mr Pronk called for security guarantees, greater disarmament and more compensation for victims.
He said the peace deal was paralysed and failed to resonate with the people of Darfur.
Only one of the rebel groups has signed the deal and many displaced people in the region reject it.
Mr Pronk was one of the diplomats who pushed the agreement through, despite objections from all but one of the rebel factions.
The weblog criticised the African Union's role in Darfur saying it lacked the capacity to implement the peace deal.
The UN is conducting the world's largest humanitarian operation in Darfur, where 300,000 people have died and a further two million people have been displaced in three years of civil war.