The Koyna region experiences 3,000 small earthquakes every year and the deep borehole experiment will try to pick up indicators to forecast quakes, Deshmukh said during Question Hour in the Lok Sabha.
"So far we have not been successful," he said adding it was not possible to put in place pre-emptive measures in respect of dealing with earthquakes.
The borehole will be laced with sensors that measure chemical, electrical and gravitational perturbations.
As the Koyna site experiences frequent earthquakes, both natural and reservoir-induced, the odds were high of observing precursors of these events.
Deshmukh replied in the negative when asked by a member whether a similar project would be taken up near Mullaperiyar dam, which has been a bone of contention between Kerala and Tamil Nadu.
In reply to a separate question, Minister of State for Earth Sciences Ashwani Kumar said five earthquakes had their epicenter in Bihar between June, 2007 and December, 2012.