"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.
"At this moment, the patient has been in an operating room at said hospital since 7:10 a.m.", the ministry said.
Garcia went into a coma after undergoing emergency surgery, local TV channel America reported.
The 69-year-old was president of Peru from 1985 to 1990 and again between 2006 and 2011.
"Others might sell out, not me", Garcia said in broadcast comments on Tuesday, repeating a phrase he has used frequently as his political foes became ensnared in the Odebrecht investigation.
Garcia is accused of receiving kickbacks from one of Latin America's largest construction firms - the Brazil-based company Odebrecht - during the building of an electric train for the Lima metro while he was president during his second term.
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 United States in bribes to officials across Latin America, including $29 million in Peru.
In November a year ago, Garcia had requested asylum at the Uruguayan embassy after a judge banned him from leaving the country for 18 months.
Garcia has repeatedly denied wrongdoing. The Uruguayan government denied the request in December.
The San Mateo County Sheriff's office said at the time it was aware that Toledo was wanted by Peruvian officials, but added that "the existence of charges in Peru alone does not authorize the subject's arrest in the United States". Prosecutors are now seeking to extend Kuczynski's detention until he can be brought to trial.