In a statement, the newspaper said the report The January night Raisina Hills was spooked: Two key Army units moved towards Delhi without notifying government has, as expected, prompted widespread reaction.
"The report is a meticulous reconstruction and a very sober interpretation of the movement of two key Army units towards New Delhi on the night of January 16-17," the statement said adding it was investigated over six weeks and written by a team headed by editor-in-chief Shekhar Gupta.
It said the report drew on highly credible sources, who had chosen to be anonymous and the newspaper is committed to protecting their identity.
The daily said it sent a detailed questionnaire to the army and the ministry of defence and accurately reported their responses in the report. These responses were reiterated by them on Wednesday.
"Neither side explained why the ministry of defence wasn't notified, why the troops were suddenly asked to go back and what explanation was offered, if any, by the Army to the Government," it said.
There are some in the government and outside who have questioned the report, even calling it "disturbing" and "baseless". All this, even those comments that attribute false motives, are, we believe, part of a necessary debate, it said.
"The Indian Express stands by the report. And in the tradition of its commitment to journalism of courage and the readers' right to know, it will continue its investigation into the events of January 16-17 and the questions these raise," it said.