In news reports afterward, Manning; his mother, Ikea Conley; and his lawyer, Lewis Small, said a female officer grabbed Manning's genitals and pulled on them during a search, causing injuries that could render him sterile.
Manning underwent surgery at Children's Hospital of Philadelphia on Jan. 8.
Ramsey said the allegations were some of the most serious that had been made during his tenure as commissioner.
"This is serious stuff," he said. "If we did something like this, then we need to get to the bottom of it real quick, and I'll take whatever action is warranted . . . but I need to know what the hell we've got."
On Thursday, Ramsey said the department had obtained Manning's medical records through a search warrant, as required by federal privacy law.
He said the records contradicted some of the allegations.
"The severity of the injuries they are claiming is not consistent with what was found," he said. "The characterization of the injury is just not accurate."
Ramsey also said police had provided the grand jury with a video that shows Manning walking out of the police station after his arrest. He says Manning appears to be uninjured, judging by his gait.
"I am not saying this boy didn't sustain some injuries somehow, somewhere. The question is whether it was at the hands of police during the course of his arrest," the commissioner said.
"The description of the action the officer is alleged to have taken - that it was incredibly violent - the information contained in his medical records does not support it."
Manning's lawyer said the severity of the injuries was beside the point.
"The fact that he had to undergo an operation is outrageous in and of itself," Small said. "The point is that the female officer had no right to touch him there. I can't conceive of anything more serious than the rights being violated in this context."
So far, Ramsey said, the department's investigation into the incident has been slowed because Manning and his mother will not talk to police.
"The problem we're having is that we can't get an actual statement from him," Ramsey said. "Everything we're getting is third party, from the media."
Small has said his clients will not speak to police unless the charges - reckless endangerment, simple assault, and resisting arrest - are dropped.
Manning and several witnesses have spoken to the District Attorney's Office, Small said, adding that he was encouraged that the office was investigating.
The department began an investigation into the incident after news reports detailed Manning's allegations.
"I want the truth to come out," Ramsey said. "Not through third parties. Not through allegations being thrown about. I want facts to drive what ultimately is decided in this case. The best way of doing that is through a grand jury."