Manikandan ran 10.60 secs in men's 100m dash, beating his Railways team-mate B G Nagaraj (10.70 secs) and Debnath Jyoti Shankar of Services (10.74 secs) to second and third places respectively.
In women's 100m sprint, Manisha Dhankar clocked 11.77sec to win the gold while her two Railways team-mates Saradha Narayana (12.03 secs) and M M Anchu (12.09 secs) were second and third respectively.
Railways top-three finish were accounted by their athletes in 100 meter dash for women and high jump for women.
London Olympian Sahana Kumari hogged the limelight improving upon her one-year-old meet mark by one cm when she cleared 1.84m.
Sahana, national record holder with 1.92m, failed in all her three attempts in the next height of 1.88m.
"I was down with fever after returning from London. It was my duty to win the event here for my department, which I justified," Sahana said after winning gold.
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Other successful title defenders include M R Poovamma in women's 400m (53.79 secs) and race walker Khushbir Kaur, both representing ONGC.
Renjith Maheswary, also of Railways, who had a disappointing outing in London Olympics, took the triple jump gold with a leap of 16.72m. It was his fifth title in the Open Nationals in his pet event.