Metropolitan Magistrate Ashok Kumar issued the warrant against Ms Patkar after a proxy counsel appearing for her sought exemption from personal appearance on the ground that she was arrested by the Indore Police last week and sent to jail.
The court fixed the matter for further hearing on September 21.
Ms Patkar's plea was opposed by advocate Mahipal Ahluwalia, representing Mr Saxena, President of Ahmedabad-based NGO National Council for Civil Liberties or NCCL, who argued that she has repeatedly remained absent for hearings.
The counsel sought a copy of the exemption application and apprised the court about the non-bailable warrant issued against Ms Patkar on the last date of hearing and imposition of Rs 10,000 as costs on her.
She was also granted a final opportunity by the court to appear before it, he told the magistrate.
"It has to be ascertained whether she has paid the amount or not," Ms Saxena's counsel said.
The magistrate had on August 3 imposed Rs 10,000 as costs on Ms Patkar for her repeated failure to appear before the court while warning her that he would dismiss her complaint against Mr Saxena if she again failed to appear.
The court had on June 26 warned Ms Patkar to be "careful in future" and had cancelled the non-bailable warrant issued against her on May 29 for her non-appearance.
It had in January 2015 also imposed Rs 3,000 as costs on Ms Patkar for non-appearance, giving her the "last and final opportunity" to present herself before it.
Ms Patkar and Mr Saxena have been embroiled in a legal battle since 2000 after she filed a suit against him for publishing advertisements against her and the NBA.
Mr Saxena, in turn, had filed two cases against her for making derogatory statements.