ATC judge Kausar Abbas Zaidi was hearing the case when the counsels of the accused exchanged hot words with the judge over withdrawal of the interim charge-sheet.
A defence counsel alleged that the court was doing the job of the prosecutor.
The ATC judge said that he could not hear the case further and went to his chamber.
Federal Investigation Agency (FIA) had submitted an interim charge-sheet, comprises of 16 pages, against three accused, Moazzim, Khalid and Mohsin, in the court hearing on April 18.
The charge-sheet delineated information about the travel history of the accused, statements of travel agents and the statements of all three accused.
MQM leader Dr Imran Farooq was found murdered near his apartment in Green Lane, Edgware, London on September 16, 2010. The case is being investigated in Landon.
FIA had also registered similar case in Islamabad in December last year, under Sections 302, 34, 109 and 120B of Pakistan Penal Code (PPC), and clause 7 of Anti-Terrorism Act.