The Pakistan Peoples Party (PPP) and Pakistan Muslim League-Nawaz (PML-N) expressed surprise and reservations over the judgement of the court, Dawn Newspaper reported.
In a statement, issued by the PPP's central media office said the verdict had baffled the party.
"Today is an unfortunate day for the rule of law," the PPP lawmaker Nafisa Shah was quoted as saying by the report.
Shah said the special court which convicted Musharraf in the high treason case last month had been constituted by the Supreme Court of Pakistan and it consisted of judges from three high courts of the country.
She was of the view that the appeal against the verdict should have been filed in the Supreme Court and not in the high court, the report said.
Shah also said that killers of former prime minister Benazir Bhutto had also not been arrested so far.
PML-N Senator Mushahidullah Khan expressed reservations over the verdict.
He said that despite the judgement, he would pay tribute to Justice Waqar Ahmed Seth, the head of the special court, which convicted Musharraf in the case.
The PML-N leader said that the whole world saw dictator Gen Musharraf" abrogating the Constitution and putting his boots on it and everyone saw the military ruler threatening and then killing Baloch nationalist leader Sardar Nawab Akbar Bugti, the report added.
The PML-N government led by former prime minister Nawaz Sharif had filed the treason case against the former army chief in 2013 over the imposition of an extra-constitutional emergency in November 2007, which led to the confinement of a number of superior court judges in their houses and sacking of over 100 judges.
Musharraf ruled Pakistan from 1999 to 2008.
Monday's ruling came in response to a petition filed by him challenging the formation of the special court for the high treason case against him.
In his petition, Musharraf asked the court to set aside the special court's verdict for being illegal, without jurisdiction and unconstitutional, while also seeking suspension of the verdict till a decision on his petition was made.
The special court had also ordered that corpse of the former military ruler should be dragged to parliament and hang for three days if he dies before his execution.
Prime Minister Imran Khan's government became furious over the ruling and said it will move to the Supreme Judicial Council to unseat the "mentally unfit" Seth, the head of the special court.
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