Additional Sessions Judge Reetesh Singh allowed Delhi Police to quiz the three — Mohammed Sajid, Shakir Ansari and Sameer — till May 14.
Police said the terror module was active and plotting to target “sensitive and crowded” areas in the national capital region.
Police had sought 15 days custody stating that some explosives had been seized from Sajid and it wanted custodial interrogation of the accused to unearth the entire conspiracy.
Defence counsel M.S. Khan opposed the plea, saying police had already recovered the materials and there was no need for custodial interrogation.
Nine suspects, with alleged links to the Pakistan-based group, were being questioned, police said.
Police said the module, which was being closely watched by security and intelligence officials for some time, was busted after separate raids in parts of Delhi and neighbouring Uttar Pradesh. An IED was also recovered from them.
Sajid, in his early 20s, is said to be one of the most wanted terrorists whose one hand got burnt while preparing a bomb sometime ago. He was arrested from Gokulpuri in east Delhi.
The other two arrested are Shakir and Sameer. They too were said to be directly linked to JeM, which was blamed for the January 2 attack on the Indian Air Force base in Pathankot.
Police said search operations were on at different places in Delhi and Uttar Pradesh.