ISLAMABAD, Pakistan — After an unexplained 13-year pause, Pakistan’s top court revived an inquiry into accusations of election rigging by the country’s main spy agency on Wednesday, but was then forced to delay proceedings when it emerged that crucial evidence was missing.

A three-judge Supreme Court bench, led by Chief Justice Iftikhar Muhammad Chaudhry, resumed hearings into accusations that the spy agency, the Inter-Services Intelligence Directorate, paid $6.5 million to a right-wing opposition alliance to influence the outcome of the 1990 election.

The case is potentially explosive in a country where the ISI has a history of meddling in politics yet its officials have largely escaped judicial censure. But analysts are divided about its chance of success.

Wednesday’s hearing was cut short after the court heard that statements recorded in 1998 by three crucial witnesses, including a former ISI chief, Asad Durrani, could not be found. A lawyer for Mr. Durrani said he was out of the country.