-LRB- CNN -RRB- -- The Humane Society has accused a federally funded primate center of mistreating chimpanzees and other primates , saying that some animals showed signs of psychosis and self-mutilation . New Iberia Research Center cages about 325 chimps on its 100 acres . It also has about 6,000 monkeys . The allegations against the New Iberia Research Center in Louisiana , which houses more than 6,500 primates , came after a nine-month undercover investigation . The center denies the allegations . `` We found animals living in isolation , exhibiting self-mutilating behavior , psychosis , all sorts of emotional and physical problems at this laboratory , '' Humane Society President Wayne Pacelle told CNN on Wednesday . The Humane Society 's undercover investigator , who worked as a laboratory technician with a hidden camera , revealed 338 violations of the federal Animal Welfare Act , which sets standards for the treatment of animals in labs , Pacelle said . The Humane Society posted some of its secret footage on its Web site . The footage includes an animal with what the group said was a self-inflicted wound , another animal jumping in circles in its cage , and chimpanzees screaming as lab technicians approached with a dart gun . The violations were filed in a 108-page complaint to the U.S. Department of Agriculture , which is required by law to enforce the Animal Welfare Act , the organization said . Agriculture Secretary Tom Vilsack said he will order a thorough investigation of animal welfare practices at the facility . `` If the allegations prove to be true , the American public can expect the perpetrators to be held fully accountable . I take the protection of animals very seriously , and will do my utmost to fully enforce the Animal Welfare Act , '' he said in a written statement . The New Iberia Research Center , part of the University of Louisiana at Lafayette , issued a statement saying that the videos `` distort acceptable standard procedures and incorrectly imply mistreatment of nonhuman primates at the New Iberia Research Center . '' It added : `` We take very seriously our responsibility to care for the animals housed at the center and to carry out biomedical research according to federal rules and regulations . '' The center further said it properly housed and cared for the animals . It also said it complies with regulations of the USDA , the Food and Drug Administration , and the Centers for Disease Control and Prevention . The Humane Society accused workers at New Iberia of hitting primates on the mouth , using `` painful '' dart guns and removing infant monkeys from their mothers . The Humane Society also said it had documented evidence of `` rampant '' breeding of government-owned chimpanzees . In 2007 , the National Institutes of Health 's National Center for Research Resources , following a 12-year moratorium , said it would no longer breed chimpanzees for research , citing financial reasons . The New Iberia Research Center has received more than $ 37 million in grants from the NIH , according to the center 's Web site . The NIH said it has opened an investigation regarding the allegations and said it is working closely with the USDA . However , it said it could not comment on the allegations while its investigation is under way . `` The results will be available when the investigation is complete , '' the NIH said in a written statement . `` We are committed to the safety and welfare of all animals in research . All animals used in federally funded research are protected by laws , regulations , and policies to ensure they are used in the smallest numbers possible and with the greatest commitment to their comfort . '' Pacelle said the most serious issue was the self-mutilation and `` nonstop pacing and circling , psychosis and other abnormal behaviors . '' `` These are highly intelligent animals . They have a sense of self , they have a sense of past and future , they have the wide range of emotions that we have , '' he said . `` They should not be subjected to this long-term , decade-long isolation , and all these painful and physical procedures and the psychological torment in these laboratories . '' The New Iberia Research Center says it offers a `` broad range of diagnostic , laboratory , and human resources for the development and characterization of nonhuman primate models for applied and basic research aimed at promoting human quality of life . '' In its statement e-mailed to CNN , the center said it has made numerous contributions to public health improvements for the prevention and treatment of three forms of hepatitis , mumps , measles , chicken pox and mad cow disease . CNN 's Bill Caiaccio and Taylor Gandossy contributed to this report .