Paul Sturrock accused referee Carl Berry of wrongly awarding a late penalty that settled the clash between Southend and Bristol Rovers.
The 86th-minute penalty earned the Pirates a 1-0 win in a closely fought encounter at Memorial Stadium.
The Southend manager insisted the two defenders who challenged Mustapha Carayol had made no contact with the Rovers winger. But referee Berry pointed to the spot and Matt Harrold fired the penalty past Cameron Belford into the centre of the goal to deal a blow to the visitors' promotion hopes.
After watching the incident again on DVD, Sturrock said: "The Rovers lad slips, rather than being brought down. I am not suggesting he was looking for the penalty, but the ref got it wrong.
"The lads are gutted in the dressing room, but we have to pick ourselves up and go again. At the start of the season we had one or two decisions like that go our way.
"There is some work to do on the training ground. We are not creating as many chances as we were earlier in the season and that is something we need to address quickly.
"We've had a few injuries and now Mark Phillips has gone to hospital with concussion. Losing him was a blow because we had to put substitute Bilel Mohsni at the back instead of utilising his attacking skills."