The ministry said Mr Garcia was still in an operating room and his condition was delicate.
Garcia had been undergoing surgery after the incident at a clinic near his home in Lima, Radio Programas reported.
Peru's former president Alan Garcia shot himself early on Wednesday after police arrived at his home in the capital Lima to arrest him in connection with a bribery investigation, a police source said.
Corruption cases have reached the highest levels in Peru politics, most notably involving officials and Odebrecht, the Brazilian construction giant that has admitted to spreading some $800 million U.S. in bribes to officials across Latin America, including $29 million in Peru.
"This morning a dramatic accident took place: the president took the decision to shoot a bullet (in the head)", said his lawyer to journalists outside the hospital.
Garcia has repeatedly denied wrongdoing.
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Mr Garcia served two terms as president of Peru, the first from 1985 to 1990 and the second between 2006 and 2011.
Peruvian presidential candidate Alan Garcia (C) greets supporters during a campaign rally in Catacaos, Piura, Peru May 30, 2006. He said that actions leading up to Garcia's arrest appeared to have been carried out irregularly.
"He entered his room and closed the door behind him", Moran said. Officers forced entry into the bedroom and found Garcia in a sitting position with a wound to the head.
Last year, Mr Garcia asked Uruguay for political asylum after he was banned from leaving the country to keep him from fleeing or obstructing the investigation. The Uruguayan government denied the request in December.
He is now under investigation after allegedly accepting bribes from Brazilian construction titan Odebrecht in return for contracts during his most recent spell in office. Ollanta Humala spent nine months in pre-trial detention in 2017-2018 and Pedro Pablo Kuczynski was arrested without charges last week.