A spokesperson for Glenister, Dani Cohen, said he had a meeting with his legal team following his failed bid in the Pretoria High Court on Wednesday, and had instructed his team to take the matter to the highest court in the country.
The Pretoria High Court on Wednesday left the door open for Glenister to take his application to the Constitutional Court, when it struck his application from the High Court roll.
Judge Willie van der Merwe said in a written judgment that the court did not have the jurisdiction to decide on the matter.
"I am furthermore of the opinion that this matter involves crucial and important political matters in which a High Court has no jurisdiction but only the Constitutional Court.
"I am therefore of the view that this court has no jurisdiction to decide the matter but that it is a matter that could possibly fall within the jurisdiction of the Constitutional Court," Van der Merwe wrote in his ruling.
Glenister told reporters outside court: "I'm somewhat disappointed ... I was hoping for a better answer ... but we obviously have to understand where the court is coming from.
"We have to look at everything the judge has written, and we have to analyse it, and then decide what our next steps are, but obviously we are not giving up," he said.
He initially brought an application asking that the court interdict President Thabo Mbeki and six others from initiating legislation that sought to dis-establish the Directorate of Special Operations or Scorpions.
Before the case could be heard, legislation was initiated by Cabinet and two Bills, the General Law Amendment Bill and the National Prosecuting Amendment Bill, dealing with the disbanding of the unit, were published.
Glenister then amended his application asking that the President and the relevant ministers be prohibited from passing the legislation.
He contended that the Scorpions had been extremely successful in combating serious crime, and said the decision to disband the unit was taken to safeguard prominent members and leaders of the African National Congress from investigation and prosecution by the unit.
The court concluded that the principle of separation of powers prevented it from interfering with the executive's power to prepare and initiate legislation, as well as with the right of Parliament to deliberate on proposed legislation brought before it.
The court further concluded that if exceptional circumstances existed - warranting interference with parliamentary procedures - it was for the Constitutional Court to decide on that issue.