The man was taken to Washington County Hospital in Hagerstown, police said.
The man was transfered to the Shock Trauma Center at the University of Maryland Medical Center in Baltimore.
A nursing supervisor said he was in critical condition Thursday night.
"My understanding is he had abdominal injuries," District Attorney John F. Nelson said.
No charges had been filed against the man as of Thursday afternoon, Nelson said.
"They did this two weeks before ... they used a crowbar to pry open the back door," Colaco said of a previous break-in in which cartons of cigarettes were taken. Three days after that, he said, an ice machine outside his store was broken into.
"I was sleeping in the store for the last two weeks," said Colaco, who is from India and has owned the business for about 1 1/2 years. When the three men entered the closed store by prying open a side door Thursday morning, Colaco said he confronted them armed with a shotgun.
"I was holding them and they tried to come right at me," he said. Two of the men came at him and "I deliberately backed off and they ran out the side door," he said.
"The third one threw a trash can at me," Colaco said.
He shot that man in the waist, he said.
"He just reached the door and ran outside and fell down," Colaco said.
The man picked up the crowbar that was used to open the door, staggered a few paces and collapsed again, Colaco said.
The store has an alarm service, which notified police, who then called the store, Colaco said.
"The first thing I told (police) was 'I need an ambulance. I just shot a guy,'" said Colaco, who was at his store Thursday.
Nelson said he met with state police and reviewed a surveillance video tape from the store, but he would not comment on whether Colaco's actions were justified.
"We're still sorting out everything that happened," Nelson said.
"The use of force upon or toward another person is justifiable when the actor believes that such force is immediately necessary for the purpose of protecting himself against the use of unlawful force by such other person on the present occasion," according to Pennsylvania law.
The General Principles of Justification, however, run for several pages, covering self-protection, protection of property, protection of other people and other situations.
"The use of deadly force is not justified under this section unless the actor believes that such force is necessary to protect himself against death, serious bodily injury" or other substantial physical harm, the section on self-protection states. The law also states that deadly force is not justified if a person can avoid doing so "with complete safety by retreating."
The next paragraph states that a person "is not obliged to retreat from his dwelling or place of work" under some circumstances.
On March 28, Colaco's store was broken into and he was armed and waiting. In that incident, Erica Marie Lynch, 19, of Greencastle, was held at gunpoint until police arrived, Colaco said.
Police said two men involved in the incident, James Byrd, 42, and Joshua L. Ingream, 21, both of Greencastle, fled. Byrd later entered a plea agreement and was sentenced to state prison in June, according to court records.
Ingream and Lynch waived their preliminary hearings last month and are scheduled for mandatory arraignment in September, according to District Attorney's Office records.
Police records state the March 28 burglary was the fourth at the store that month.