The plea was rejected by Principal Judge P B Desai, presiding over the Special NIA Court here, after the accused - Haji Patel, Mohammad Yunus Shaikh and Abid Patel - declined to give consent to undergo polygraph test.
During arguments today, their lawyer citied various orders of the Supreme Court as well as High Court in this regard and argued that consent of the accused is necessary to conduct lie detection test.
As the Central agency did not seek further remand, the court sent all the accused in 14-day judicial custody.
The two BJP leaders - Shirish Bangali and Pragnesh Mistry - were shot dead by two unidentified gunmen in Bharuch, about 200km from here, on November 2.
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Bangali was a former President of Bharuch district unit of BJP, while Mistry served as General Secretary of Bharatiya Janata Yuva Morcha.
Initial probe by Gujarat Police revealed the contract for killing the BJP leaders was given allegedly by fugitive underworld don Javed Chikna, apparently to avenge communal riots in Mumbai and Gujarat in 1993 and 2002, respectively.