Heavy police force was deployed on the court premises as well as in parts of the city following the incident.
"Qureshi was shot three times in the neck from point blank range on the district court premises when he was being taken for a hearing," Additional Superintendent of Police (ASP) Neeraj Soni said.
The two accused, identified as Prashant Sahu and Dharmendra Malviya, were arrested, he said adding, "Prima facie, it appears that the incident was fallout of some old rivalry. A probe has been launched into the incident," he said.
Mr Soni said that security has been beefed up on the court premises along with different parts of the city after the incident.
Ikhlaq, who was former city president of the BJP's Alpsankhyak Morcha (Minority Cell) was an under-trial prisoner as he was accused in several cases, including in the alleged attack on Shiv Sena leader Narendra Patel.
BJP's state minority cell president, Sanwar Patel, confirmed that Qureshi was a former city unit chief of the party's minority cell.
"The incident is unfortunate. Presently, there is no executive body of minority cell in Chhindwara city. Qureshi was former city president of the minority cell," Mr Patel said.
Meanwhile, the Congress slammed the state government for the "deteriorating" law and order situation in Madhya Pradesh.
The incident in Chhindwara shows that people are not safe even on the court premises. Such incidents are creating panic across the state," state Congress spokesperson Pankaj Chaturvedi said.