"There's no evidence that Avonte is not alive," family attorney David Perecman said, adding he was stunned by Kelly's remarks on Thursday night.
"I'm going to ask the commissioner not to make statements like that," Perecman said. "The family had no idea it was coming and they were really hurt when the statement was made."
Kelly's statement came during a brief interview with reporters.
"Obviously we have devoted a tremendous amount of resources to the search," he said. "Unfortunately, we are not hopeful that we're going to find this young man alive, but we are continuing our search."
Concerned perhaps that Kelly was suggesting the search may be scaled back, Perecman pressed for investigators to not scale back their search, but do things not yet attempted.
"The main purpose is to bring life and rejuvenate the effort as it gets cold to find Avonte," he said. "Anything that anyone says or does to dampen the effort to search for Avonte is inappropriate, reckless."
"I want them (police department) to continue searching," his mother, Vanessa, said.
"Hopefully, (Kelly's) comments will encourage more people to come out and volunteer," added his father, Daniel Oquendo, Sr.
The number of volunteers appears to be dwindling and the boy's family is encouraging people to please come out and help with the search. The National Action Network is gearing up for a major push this Sunday.
When interviewed by reporters Friday, the police commissioner changed his response.
"We are continuing to devote significant resources to the effort," Kelly said.
"Do you think he could still be alive?" a reporter asked.
"You know, we certainly hope so," Kelly said.
Kelly says investigators have chased down 450 leads and reviewed nearly 200 pieces of video, but so far none of it has led to Avonte.
Even as the temperatures start to plummet, Kelly said on Thursday that the search will still continue throughout the northeast and he encouraged anyone with information to contact police.
"We are continuing to put information out," he said. "We're talking to jurisdictions in the northeast quadrant of the United States. We ask anyone with any information to call our TIPS hotline."
For the past three weeks, volunteers, police officers and Oquendo's friends and relatives have exhaustively searched and painted the city with flyers.
The boy was last seen on October 4 leaving his school in Long Island City, and a massive manhunt ensued. Unfortunately, all the manpower, effort and energy has turned up nothing thus far.
Police say Avonte was fascinated with trains and had previously turned up at subway stations after wandering off from home, so that is where investigators are focusing their energy.
Most recently, in August after he wandered away from home, family members ran to the 67th Avenue Station in Forest Hills where they found him.
Five years ago, he took the subway from Jamaica to Kew Gardens/Union Turnpike Station. Transit police found him that time. And seven years ago, he was found at the Fresh Pond Road Station in Ridgewood after wandering from home.
The reward for Avonte's safe return is up to nearly $90,000.