The arrests were made early Sunday morning as the fire still raged, but police did not announce them until the cause of the fire at 111 Congress St. was determined.
Christopher Kelly, 16, of George Street, is being held in the Albany County jail without bail after his arraignment on one count of second-degree arson and three counts of second-degree assault, all felonies.
The other boy, who is 15, is being treated as a juvenile and his case will be heard in Albany County Family Court. He was ordered held in a secure juvenile facility.
Detective Lt. Thomas Ross said the two teens were taken into custody within minutes of police arriving at the scene of the fire. "They gave us statements as to their involvement," but they gave no indication as to why they burned the building, he said.
While they had the admissions from the youths, police still wanted to get an official cause, Ross said. Investigators have now labeled the fire an arson, he said.
The assault charges were lodged because three firefighters suffered minor injuries fighting the fire, Ross said. The teens also admitted to setting a couch on fire in an alley about two blocks from the apartment building just after 11 p.m. Saturday. The apartment building fire was discovered at midnight, Ross said.
According to Ross, the teens said they brought a change of clothes with them "in case they were spotted by a witness" and changed their shirts between the two fires.
Neighbors and the building's owner, Matt Ryan, said the building had been a gathering spot for young people.
The building sustained extensive damage from the fire. Ryan said he did not have insurance on the structure, but there was a policy held by a bank involved in the real estate dealings.
Ross said the investigation remains open with several more interviews to be done.