A 14-judge bench, headed by Chief Justice Tassaduq Hussain Jillani, said the time period for filing an appeal has lapsed.
It further said the review petition was not maintainable as it did not fulfil the criteria of merit. The bench said arguments presented by 70-year-old Musharraf were irrelevant to the case.
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In an order issued in July 2009, the apex court had declared the emergency proclaimed by Musharraf in November 2007 as unconstitutional.
On December 23 last year, Musharraf filed a petition after a delay of over four years seeking a review of the apex court's verdict.
The petition stated Musharraf was facing trial in a special court on charges of high treason on the basis of the apex court's July 2009 order.
The petition argued that former Prime Minister Shaukat Aziz had recommended taking extra-constitutional measures to proclaim an emergency in 2007.
Musharraf's lawyers had repeatedly sought time from the special court trying him for treason on the ground that the apex court was yet to decide his review petition.
The former army chief was admitted to a hospital in Rawalpindi in January 2 after he developed heart problems while being driven to the special court.
During today's hearing in the Supreme Court, Musharraf's counsel Sharifuddin Pirzada said unconstitutional steps had been taken several times in Pakistan's past and the judiciary had endorsed these steps on important issues.
To substantiate his claims, Pirzada also gave the example of emergency being imposed in Canada and India.
On hearing this, Justice Jawad Khawaja asked if constitutional provisions on treason were applicable in Canada, and Pirzada replied they were applicable in Canada and a few other countries.
Musharraf is the first military ruler to be put on trial for treason in Pakistan's history. If convicted, he could face life imprisonment or the death penalty.