Bognor boss Michael Birmingham accused Newport County of intimidating the referee as the Rocks slipped closer to the relegation zone.
Birmingham was sent to the stands in the second half after County had taken the lead from a dubious penalty and Bognor were denied a spot-kick of their own moments later.
Former Wales international Jason Bowen made no mistake from 12 yards and Lee Fowler made it 2-0 in the 63rd minute.
Birmingham said: "Andy Pearson definitely handled the ball for their penalty but he was given a huge shove in the back and at the other end Dan Beck's cross clearly hit their defender on the arm but nothing was given.
"The referee gave them the decision because he was intimidated by their players but I don't want to say anymore about him because I'll get myself in trouble."
Birmingham is hoping to sign a striker before today's transfer deadline following Luke Nightingale's move to Havant and Waterlooville.
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