The 'A' samples of the four were found to have contained Stanozolol and Methandienone anabolic steroid and Methylhexaneamine stimulant.
Three of them who had tested positive for steroids have been provisionally suspended.
National Anti-Doping Agency Director General Rahul Bhatnagar said that the samples were collected from the athletes who participated in discus throw, javelin throw and hammer throw in the April 21-23 Championships.
He said that the athletes caught for doping belong to Punjab and Allahabad and there were no big names involved.
"During the 16th Federation Cup National Senior Athletics Championships, NADA had organised Dope Control Programme and collected 47 samples. According to the analytical reports of sample received from National Dope Testing Laboratory (NDTL), four samples out of 47 have been found containing prohibited substances notified by World Anti Doping Agency (WADA)," Bhatnagar said.
Athletics was hit hard by one of the biggest doping scandals last year when six top athletes, including Asian Games double gold-medallist Ashwini Akkunji was caught for using banned steroids.