The commission will travel to Karachi on October 6 to examine the boat, Al-Fouz, and will also record the testimony of a witness who saw the vessel being seized at the Karachi Shipyard.
Headed by an ATC judge, the commission includes officials from Federal Investigation Agency (FIA), the defence counsel and court officials.
The commission was constituted during a hearing into the Mumbai terror attacks case by ATC-Islamabad, which held the hearing at the Adiala Jail Rawalpindi, last week as the court heard the boat was used by the terrorists in the attacks in which 166 people were killed and around 300 were injured.
The ATC judge accepted the request by the FIA to send a judicial commission to examine the boat as it was difficult to produce the vessel before the court.
Earlier the Islamabad High Court had set aside the verdict of a trial court of not allowing to send a commission to Karachi terming it "flawed and not in accordance with law" and allowed examination of the boat in the port city.
In May, the prosecution had challenged the trial court's decision to reject its plea to form a commission to examine the boat so that the vessel could be made a "case property".
Al-Fauz is in the custody of Pakistani authorities in Karachi, from where the 10 LeT terrorists armed with AK-47 assault rifles and hand-grenades had left for India on November 23, 2008, to carry out attacks in Mumbai.
En route to their destination, they hijacked another boat, killing four of its crew members. They forced the vessel's captain to take them close to the Indian shores and killed him when the vessel reached Mumbai's coast.
Mastermind and LeT operations commander Zaki-ur Rehman Lakhvi, Abdul Wajid, Mazhar Iqbal, Hamad Amin Sadiq, Shahid Jameel Riaz, Jamil Ahmed and Younis Anjum are accused of abetment to murder, attempted murder, planning and executing the Mumbai attacks.
Lakhvi is living at an undisclosed location after being released from jail on bail a year ago. The other six suspects are in Adiala Jail, Rawalpindi. The case has been underway in the country for more than six years.