"This is a fabricated story prepared by the police and I don't believe it," said Qamar Sheikh, mother of Sheikh Abdul Nayeem.
He could have been, instead, killed in an encounter by the police, said the letter.
"My son was under treatment for kidney disease and had become weak (to have fled). Given all the circumstances there is a possibility that he may have been killed in an encounter or illegally detained and as a mother I fear for his life and safety," said Qamar.
According to the police Nayeem jumped off the Howrah-Mumbai mail between Kharsiya and Shakti railway stations in Chhattisgrah on Sunday.
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Qamar has sent copies of the letter to Bombay High Court, Calcutta High Court and Andhra Pradesh High Court and the trial court here.
On May 8, 2006, a Maharashtra Anti-Terrorism Squad chased a Tata Sumo and an Indica car on Chandwad-Manmad highway near Aurangabad in Maharashtra, and arrested three terror suspects and seized RDX, AK-47 rifles and live rounds.