Days after a 1-year-old died and three children exposed to drugs at a Bronx day care site were hospitalized, investigators uncovered a trap door under a play area that was concealing fentanyl, other narcotics and drug paraphernalia.

The police had already discovered a kilogram of fentanyl near nap mats at Divino Niño on Morris Avenue, but the new search was triggered by a tip that more drugs had been hidden, Lieutenant John Russo said on Thursday. A neighbor had said last week that the owners of the facility had spent months sprucing it up — including laying down new floors.

On Saturday, the day care program’s operator, Grei Mendez, and a tenant, Carlisto Acevedo Brito, who lived in the apartment, were both arrested and charged with murder in the death of the toddler, Nicholas Feliz Dominici, as well as criminal possession of drugs and other related charges. In addition to the kilogram, the police had already recovered two so-called kilo presses used by drug dealers to package large quantities of drugs.

As of Thursday afternoon, the medical examiner’s office had not made an official determination of the cause of Nicholas’s death following an autopsy on Saturday. Fentanyl was found in the systems of the three children who were sickened.

The day care site, in the north Bronx, is among the areas hardest hit by fatal overdoses in the city. There were 2,668 fatal overdoses in the city in 2021, reaching “unprecedented levels,” according to data released this year. The increase was driven by fentanyl, a synthetic opioid that was involved in 80 percent of overdose deaths that year, and residents of the Bronx had the highest rate, the city found.

Ms. Mendez, a citizen of the Dominican Republic who has lived in the United States for nine years, and Mr. Acevedo Brito are also facing federal charges of one count of possession with intent to distribute narcotics resulting in death and one count of conspiracy. The police are still searching for a third person wanted in the case, Lieutenant Russo said on Thursday.

Ms. Mendez was renting a room to Mr. Acevedo Brito, who is her husband’s cousin, for $200 a week, her lawyer, Andres Aranda, said during her arraignment in Bronx Criminal Court on Sunday, adding that there was no indication she knew anything about the drugs.

“Her only crime is renting a room,” he said.

Federal prosecutors said that Ms. Mendez called her husband twice before calling 911. A federal criminal complaint said that before emergency personnel arrived, the husband entered the apartment empty-handed and left about two minutes later carrying two shopping bags weighed down by their contents.

On Thursday, members of the Police Department’s crime scene unit had taped off the area. Children played on the sidewalk and stood by the apartment building, where candles, flowers and a teddy bear were left outside the front door. Investigators in white hazmat suits and industrial-grade masks entered the building and walked out hauling brown evidence bags.

The tip the police received gave specific instructions on where to find the trap door and how to access it, Lieutenant Russo said. A photo released by the police showed a storage compartment about four feet by six feet under a splintered wooden door. Large, clear storage bags filled with narcotics, as well as red Target shopping bags, were visible in the cache under a gray linoleum floor. A shelf holding toys was nearby.

Officials said the day care program was licensed in May to serve up to eight children at a time by the state’s Office of Children and Family Services after passing two inspections. In addition, a surprise inspection this month found no violations.

Investigators this week said they were working with federal authorities to determine whether Divino Niño was a front for a drug operation.

Silvia Leal, 65, who has lived in the Bronx for 30 years and operated a day care program before retiring, said she found the situation suspicious.

“For someone to open a day care in the United States you have to take classes, there is paperwork, your fingerprints get lifted, you have to have start-up capital and there are a lot of details and requirements,” she said. “For her to open a day care so quickly in this neighborhood, someone had to have given her money.

“They were using that day care to cover something up,” she said.

Wesley Parnell contributed reporting.