"We have filed a writ petition in the Islamabad High Court challenging the formation of the special court. They are not competent to try Musharraf," Mohammad Ali Saif, chief of his legal team, said.
The move came three days before the 70-year-old former president was to appear before the special court.
This is the first time in Pakistan's history that a former military dictator is facing trial for treason. If convicted, Musharraf could face either life imprisonment or the death penalty.
"Being an Army officer, the Pakistan Army Act 1952 is applicable to him," Saif told PTI, explaining why the special court was not competent to try Musharraf.
The writ petition said Musharraf took the decision to impose the emergency on November 3, 2007, while he was the army chief. It said the decision was not an individual act and hence cannot be tried alone.
The petition stated that the government is pursuing Musharraf's cases to further a political agenda.
Musharraf's legal representatives in London have already submitted a report to the UN high commissioner for human rights and have appealed to the US, the UK and Saudi Arabia to help the former military ruler.
His legal team has called on the international community, in particular the British, the US and Saudi governments to intervene in support of Musharraf who has provided immense assistance to the West in its "war on terror".
The special court was set up by the Pakistan government to try Musharraf for high treason for suspending the constitution in 2007.
The former president is charged with abrogating, subverting, suspending, holding in abeyance and attempting to conspire against the 1973 Constitution by declaring emergency and overthrowing the superior judiciary.
On November 17, the government decided to initiate treason proceedings against Musharraf.
Attorney General Munir Malik has said there is strong evidence against Musharraf and he could be sentenced to death or life imprisonment.