The reason for Judge Chaudhry Habib-ur-Rehman going on leave could not immediately be ascertained.
Court officials said the case would be taken up again on May 25.
The Federal Investigation Agency is yet to appoint someone to replace chief prosecutor Chaudhry Zulfiqar Ali, who was gunned down by suspected militants in Islamabad on May 3.
Sources said Ali's deputy Chaudhry Azhar too was not keen on handling the case following the assassination of the chief prosecutor.
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No group claimed responsibility for the attack.
Besides the Mumbai attacks case, Ali was also handling the Benazir Bhutto assassination case, over which former President Pervez Musharraf was recently arrested by the FIA.
The seven Pakistani suspects have been charged with planning, financing and executing the attacks that killed 166 people in Mumbai in November 2008.