Chief judicial magistrate SS Thakur issued the production warrants against Nagori, his brother Kamruddin, Aamil Pervez, Asif Hussain and Sibli here following an application by Gujarat police, prosecutor A K Choure told PTI.
Nagori is in Rewa Jail, while the other four are lodged in Indore prison, police said.
Armed with the warrants for taking the SIMI leaders to Gujarat under transit remand, Gujarat police team has gone to Indore for securing their custody.
The police team comprising 40 commandos will take the SIMI leaders by air to Gujarat, police said.
Soon after the Gujarat police accused Nagori and certain other SIMI activists of involvement in the serial blasts, a team of Gujarat police officials reached Madhya Pradesh to probe the connections.
Gujarat police claimed that Nagori and Kamruddin had hatched a conspiracy during "training camps" in Halol, Gujarat and Kerala for carrying out serial blasts in Gujarat.
Earlier, in March, Nagori along with 12 other SIMI activists were arrested from a house in Indore where they had gathered for a crucial meeting of the banned outfit.
They are currently lodged in various jails in Madhya Pradesh, police said.