Nissan, which owns a majority stake in the Renault-Nissan plant near the city of Chennai, said it was working with stakeholders and coordinating with the union to reach an amicable resolution.
"We are gradually ramping up our production capacity in both Line 1 and Line 2," Nissan told Reuters.
The guidelines apply to all carmakers including Ford and Hyundai. However, only the Renault-Nissan factory will be inspected as unions at other automakers have not raised objections, the court said.
The DISH review last week had also found that three in four workers at the plants had not been vaccinated, one in seven workers had contracted the virus, and 21 had died.
Workers at the three plants accounted for more than 4% of all active cases in the two districts where the plants are located, according to the report dated June 18.
Still, Tamil Nadu on Sunday allowed some industrial units including those of global automakers in and around capital city Chennai to operate at 100% capacity, citing a decline in cases.
New cases in the state have fallen from more than 30,000 a day in May to about 7,000, but still account for one-ninth of all cases in India.
The DISH report showed that output of the three carmakers was nearly two-thirds that of pre-lockdown levels, and average attendance as on June 17 was about 90%.
Renault-Nissan on Tuesday sought to discontinue the practice of deploying an empty slot on the conveyor belt - a change that would help the carmaker increase production - as it was found to be ineffective in maintaining social distancing.
"I respectfully submit that this would be identical to the business operations adopted in all other similar car manufacturers like Hyundai and Ford," Renault-Nissan said in a court filing reviewed by Reuters.
Production at the Renault-Nissan plant was nearly three-fifths of pre-lockdown levels on June 17, when DISH conducted the review.
Renault-Nissan workers have been pushing for an empty slot for every slot on the conveyor belt with a car, and for the reduction in conveyor belt speed, saying it hindered maintenance of social distancing.
"The non-availability of sufficient time in some stations leads to the carry-over of the unfinished job to the next station and causes overlapping," the union said in its court filing, citing the DISH report.
(Reporting by Sudarshan Varadhan, editing by Robert Birsel and Louise Heavens) ((Sudarshan.Varadhan@thomsonreuters.com; +919810393152; Twitter: https://twitter.com/sudvaradhan @sudvaradhan;))