With a flawless round of four-under 68, Perera totaled ten-under 216 and went one clear of his compatriot and overnight joint leader Anura Rohana.
Rohana stayed in the hunt with a round of three-under 69, and is the leading professional in the field. Kunal Bhasin is at third place, with a tournament total of four-under 212.
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Mandeo Singh Pathania returned the best card of the day, shooting 66 and is on the fourth position tied with Harinder Gupta and defending champion Shamim Khan.
Local pro Deepak Thapa Magar, the 2007 winner, emerged best among locals tied for seventh, eight shots off the lead. Shiva Ram Shrestha threatened to storm ahead, and at one point was four-under for the round after seven holes. But, a disastrous eight hole, where he made a quadruple bogey, knocked the winds off his sails and he finished with a round of two-over 74.
No Nepali golfer stands a realistic chance of winning the title going into the final day and receiving the trophy from President Dr Ram Baran Yadav on Saturday.
Scores after Day III: 206: Mithun Perera; 207: Anura Rohana; 212: Kunal Bhasin; 213: Shamim Khan, Harinder Gupta, Mandeo Pathania; 214: Deepak Thapa Magar; 215: Nabin Mondal, Ramesh Kumar; 216: Ashok Kumar, Ram Thapa; 217: Siddikur Rahman, Shiv Ram Shrestha, Ramesh Nagarkoti; 218: Rafick Ali
