The 51-year-old Mukesh (61-68), who had blasted a phenomenal nine-under-61 on day one, kept his overnight four-stroke advantage intact with a total of 11-under-129.
Gurgaon's Deepinder Singh Kullar (65-68) and Delhi's Honey Baisoya (67-66) shared second place at seven-under-133.
Mukesh had a slow start to the day when he three-putted for a bogey on the 11th. He then missed a 15-footer for eagle on the next but still managed a birdie there. Another birdie and bogey on the 14th and 16th meant that he made the turn at level-par.
Mukesh said, "My putting let me down today. I didn't have the same rhythm on the greens as I did during round one. I wasn't stroking it well. I was thrilled with my chip-in birdie on the fifth where I recovered really well after first landing it in the rough and then in the bunker.
He added, "I feel a total of four to five under over the last two days will give me a very good chance of winning the title. I say this because there's pressure in the last two rounds and those behind me would have to play out of their skins to shoot really low scores to catch up with me.
Earlier in the day, Deepinder Singh Kullar, who was overnight second, ended the day with a 68, while Honey sank six birdies against two bogeys for his 66 in round two to join him in second place.
Lucknow's Sanjay Kumar and Bangladesh's Md Zamal Hossain Mollah occupied tied fourth place at five-under-135.
The cut was declared at five-over-145. Fifty-four professionals made the cut.
Professional C Arul (70-73) was the only Chennai-based player to make the cut. He was placed tied 37th at three-over-143.
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