The defence ministry had initially declared Sunday's test of India's longest-range missile a success, but it plunged into the ocean in the Bay of Bengal, short of its target.
Terming the failure a snag, the minister, Pranab Mukherjee, told reporters late on Sunday that India would press ahead with the programme and correct the faults.
He did not say what had gone wrong, but Indian media reported that the missile's second stage did not separate during flight.
Citing unnamed ministry officials, the Hindustan Times newspaper said the problems were caused by a design flaw.
Ministry officials could not immediately be reached for comment on Monday.