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Judicial Magistrate Ajay Singh Thakur granted her bail on a security of Rs 10,000 in the 13-year-old case.
Bharti, wearing saffron robes, first appeared in the court of Chief Judicial Magistrate Bhubhaskar Yadav, but as he was on leave, she approached Magistrate Thakur for bail.
Her lawyer Harish Mehta said the minister could not appear on the last date, September 29, as she had to chair an urgent meeting regarding the Cauvery water-sharing dispute between Karnataka and Tamil Nadu.
On September 29, CJM Yadav had issued a non-bailable warrant against Bharti for not appearing before the court since October 2015.
The district court stayed the warrant on the same day.
The Congress leader dragged Bharti to court alleging defamation in 2003 when she, as BJP's chief ministerial candidate during the Madhya Pradesh Assembly polls, alleged that a multi-crore rupees scam had taken place during Singh's tenure as the chief minister between 1993 and 2003.
Earlier this year, the CJM's court had asked Bharti and Singh to attempt mediation to settle the dispute out of the court, but it did not work out.
(Reopens LGB 4)
Bharti later said she would not tender apology to settle the dispute amicably.
"Digvijaya is my elder brother. I will feel happy if he withdraws the case," a press release issued by her office quoted her as saying.
"I respect the court and will furnish facts regarding the case. In respect of the tricolour and on corruption and moral values, I cannot compromise," she said.
The Union minister said she had faced action for unfurling the national flag (at Hubli in 2004), her involvement in the Ram Mandir movement, etc.
"That is why I don't consider myself a criminal and if necessary, I will proudly continue to commit such crimes often," she added.