The 20-year-old Indian, who shared the overnight lead, was placed second. He is one shot behind overnight co-leader Thailand's Jazz Janewattananond (66-67).
At 10-under, Shubhankar, who was third at the same event last year, was two clear of third placed Thai duo, Rattanon Wannasrichan (70-64) and Panuphol Pittyarat (66-68).
Despite giving away some shots, Shubhankar said he was satisfied that he had reached his first goal. "My target was to shoot 10-under for the first two rounds and I managed to do it. I am looking forward to the next two rounds."
Also making the cut at the halfway stage were Rashid Khan (73-67) at Tied-18th, Honey Baisoya (70-73) and Sujjan Singh (72-71) are Tied-36th while Jeev Milkha Singh (74-70) and Mukesh Kumar (70-74) are Tied-50th and M Dharma (74-71) is Tied-64th.
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Ten Indians made the weekend rounds but four golfers -- Ajeetesh Sandhu, Kapil Kumar, debutant Arjun Prasad and C Muniyappa missed the cut.
Shubhankar had mixed feelings about his round. "The round wasn't as smooth as it was yesterday but it was still a good round. I hit the ball decent although I would like it to be better. My ball striking today was not too bad. I made less birdies and two bogeys which I shouldn't have made. It could have been easy pars."