It wasn't immediately clear how the high court's ruling would play out.
Pakistani authorities also have an inconsistent track record in enforcing court decisions against prominent figures. A January court order for the arrest of Prime Minister Raja Pervez Ashraf in connection with a long-running corruption case has yet to be carried out.
No former Pakistani army chief has been arrested before, and former presidents have only ever been placed under house arrest, never sent to jail.
When asked last week about his fears of arrest, Musharraf brushed the question aside.
He had previously received bail extensions in the cases concerning him. And he was initially granted "protective" bail to ward off potential arrest when he returned to Pakistan. But the judiciary appears to have taken a more aggressive line than he may have expected, stepping up the pursuit of cases against him.
Accusations over Bhutto
Besides the case concerning the detention of the judges, Musharraf is also accused separately of not doing enough to protect the life of Benazir Bhutto, the first woman to be elected prime minister of Pakistan. A leading member of the opposition, she was assassinated on December 27, 2007, after leaving a campaign rally in Rawalpindi, just two weeks before the general election in which she hoped to be returned to office.
In another case, he is charged with ordering his troops to kill Nawab Akbar Bugti, a popular tribal leader in the volatile province of Balochistan, in 2006.
Musharraf was disqualified from contesting elections in Pakistan because of the state of emergency he declared in 2007. Even though he hasn't been tried for that action, the move was ruled an act of treason, making him ineligible to run for office. Musharraf maintains he should not be barred because he has not been convicted of any criminal acts.
Some Pakistanis are happy to see the return of the ex-military ruler, hoping his leadership could help restore order to a country riddled with political division and plagued by extremist violence.
But he also made many enemies in the final years of his presidency, notably among the judges he detained.
The Pakistani Taliban vowed to send a death squad to hunt down the former president if he returned to the country.
Musharraf has said he has been living under threats of death since September 11, 2001, when he supported the American war on terror and fought against the Taliban.
The former general became president after a bloodless coup in 1999.
Musharraf's popularity began declining in 2007 after he suspended the nation's Supreme Court chief justice for "misuse of authority." The move resulted in protests and accusations that he was attempting to influence the court's ruling on whether he could seek another five-year term.