Sessions Judge K K Tantrapale rejected Jundal's plea, special prosecutor Ajay Misar told reporters.
Bilal Shaikh, Himayat Baig and Abu Jundal have been arrested in the case. Baig was sentenced to death in Pune's German Bakery blast case last week.
Maharashtra Anti-Terrorism Squad earlier this month filed chargesheet in the present case, which relates to an alleged plot to attack Maharashtra Police Academy here in 2010.
Misar argued before the court that Jundal was actively involved in the conspiracy.