He shot one-over 72 and stood four strokes behind overnight leader, Jazz Janewattananond.
Both Jazz and Shubhankar are looking for a breakthrough Asian Tour victory at the Kurmitola Golf Club.
Shubhankar tried to shrug aside the struggles of back nine as he said, "It was a really interesting round. I had a superb start but fell back on the back nine. Other than that, I think I still played pretty well. I am still swinging the ball good.
"The dropped shots were costly but I am still in a good position for tomorrow, although I would have liked the gap to be closer. It's not over yet. I still have another round so I will do my best."
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Indians had a strong presence on the leaderboard as Chiragh Kumar (68) was Tied-fifth and Udayan Mane (68) moved up to Tied-eighth.
The 20-year-old Indian was leading the field by two after being three-under for the front nine as Jazz was even par. But he had triple bogey on 11th but quickly made some ground with birdies on 13th and 14th.
However, he again gave away a bogey on 16th and a double bogey on 17th to end at 72.
Jazz, meanwhile, calmly slotted two birdies against no bogey on back nine to take a big lead.
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