During the hearing, Captain Amit Tyagi's counsel told Justice Vibhu Bakhru that the pre-flight BA test showed the reading between 0.16 and 0.20, which was below the international permissible standard of 0.40.
Aviation regulator Directorate General of Civil Aviation (DGCA), which suspended Tyagi in May 2018, told the court that its standard for permissible alcohol level was zero.
The suspension order was upheld by the Civil Aviation Ministry in April this year.
The suspended pilot has stated that he had get a blood test and urine test conducted in a private lab immediately after the BA test and it showed no alcohol in his system.
The DGCA countered saying that the pilot had once tested alcohol positive in the past and had then claimed it was due to consumption of cough syrup.
Justice Bakhru asked whether application of cosmetics containing alcohol would show up in the BA test.
The court further questioned if the BA test will catch alcoholic "remnants of this nature even in application of perfume".
The court has sought a response from the DGCA and the Civil Aviation Ministry, listing the matter for further hearing on August 13.
The pilot's counsel also told the court that the entire calibration of the breath analyser was faulty as according to standards it should be re-calibrated every 30 days.
( With inputs from IANS )