WARREN — An 18-month-old boy is in a Portland hospital with potentially permanent brain injuries after he was assaulted Saturday by his mother’s boyfriend, police say.

Joseph K. Emerson, 24, was arrested Monday evening on two counts of aggravated assault against the boy. The other allegedly occurred on June 21, and it also caused injuries, according to court documents.

The child suffered a fractured skull, bruised brain and four broken ribs in Saturday’s assault, according to an affidavit filed in Knox County Court by Maine State Police Detective Scott Quintero. The child now faces developmental disabilities because of the injuries, District Attorney Christopher Fernald told Judge Susan Sparaco.

The boy was taken to Maine Medical Center in Portland on Sunday morning. Medical staff alerted Maine State Police after concluding his injuries were not consistent with how his mother initially said he got them.

The boy’s mother told police she had left him with Emerson, her boyfriend, when she went to work Saturday, according to the police affidavit. When she returned home that evening, Emerson told her the boy had fallen off a metal chair and struck his head. Emerson told her the boy’s eyes had rolled back into his head for a moment but then returned to normal.

Emerson, who is not the boy’s father, said he applied ice to the boy’s head to reduce the swelling, according to the affidavit.

The mother told police she did not believe Emerson was violent with the boy, but also said she had seen him treat the child roughly, including squeezing him around the ribs hard enough that the veins in Emerson’s arm bulged.

The mother called the child’s father the following morning when the boy awoke and was not acting right, according to the affidavit.

Medical personnel told police that the boy’s injuries could not have occurred in the manner she described.

In addition to the skull fracture, the child had a bruised brain, which a doctor said would likely lead to developmental disabilities. The child also had four broken ribs that were 1 to 2 months old, and a lacerated liver. Police said a prior assault on the child occurred on June 21.

State police interviewed Emerson on Monday and he initially repeated the story about the child falling off the chair. He then changed his story and said he had dropped him.

Eventually, Emerson told police he threw the child off the bed because the boy was hitting him with a toy truck, according to the affidavit.

Emerson remains at the Knox County Jail in Rockland in lieu of $50,000 cash bail.

Defense attorney William Pagnano asked that Emerson be released on $1,500 cash bail. Pagnano said Emerson was a lifelong resident of Knox County, had family locally, had a steady job and no criminal record other than an illegal attachment of license plates.

Fernald said, however, that Emerson would be a flight risk since the Class A aggravated assault charge carries a potential prison term of 30 years.