Forty-nine children died and more than 70 were seriously injured when flames spread through the ABC nursery, which did not have an emergency exit.
Relatives of the victims have long demanded justice saying the nursery did not comply with safety regulations.
But a lawyer for the relatives said the warrants targeted the wrong people.
Prosecutors asked a judge to issue the arrest warrants for the director of the nursery and some of its management and teachers.
Gabriel Alvarado, a lawyer for the relatives' group Hands United for Our Children called the move "erroneous" arguing it did not target the officials responsible for the tragedy.
He said it could punish those who had risked their own lives, and in some cases had suffered injuries, trying to save the children.
Mr Alvarado added that one of the teachers who could face arrest has a daughter who suffered burns to 95% of her body in the fire.
"This girl could now see her own mother taken to prison," he said.
The fire started at a warehouse in the city of Hermosillo on 5 June 2009.
The flames quickly spread over a roof to the adjoining nursery, where the children where having their afternoon siesta.
The nursery did not have a sprinkler system or any fire extinguishers.
The smoke alarms were faulty and the staff were poorly trained.
Victims' relatives argue that the tragedy could have been prevented if the right safety measures had been in place.
They also point to the fact that a nursery should not have been housed in a building adjacent to one storing tyres and flammable materials.
They are angry that while dozens of officials were put on trial, only the government official who carried out the nursery's final safety inspection has spent any time in jail.
Their anger is further compounded by a media report published last year alleging that the fire in the warehouse may have been deliberately caused to get rid of compromising local government documents stored there.
The official report concluded it had been triggered by a short circuit.

Simon Cope delivered the package on the last day of the 2011 Criterium du Dauphine, which Wiggins went on to win.
The Culture, Media and Sport select committee has been by told by Team Sky chief Sir Dave Brailsford the package contained a legal decongestant.
But MPs say they are "concerned" by some of the evidence they have heard.
The doctor who received the package on behalf of Wiggins' Team Sky, Dr Richard Freeman, and head of UK Anti-Doping (Ukad) Nicole Sapstead have also been invited to give evidence on 22 February.
Culture, Media and Sport select committee chairman Damian Collins MP said: "There is a considerable public interest in Ukad's investigation and it is also important to our inquiry into doping in sport to understand what they have been able to determine from their investigation.
"The committee has been told by both British Cycling and Team Sky that they have supplied all the information they have relating to this investigation to Ukad.
"However, we need to know if they have received documentary evidence which confirms what was in the package that was delivered by Simon Cope to Team Sky.
"Without this evidence, I am concerned about how it is possible for the anti-doping rules to be policed in an appropriate manner, if it is not possible to review the records of medicines prescribed to riders by the team doctors."
Team Sky have been under pressure to reveal the contents of the package following a Daily Mail allegation in October 2016.
Cope, who was a women's coach for British Cycling, travelled from Manchester to Geneva on 12 June 2011 to hand a parcel to the Team Sky doctor Freeman on the final day of the Criterium. Cope claimed he did not know what it contained.
In an interview with Cycling News, he said: "It was just an envelope, a Jiffy bag, a small Jiffy bag," he said. "As far as I know I could have been pedals in there."
Brailsford gave evidence in December and stated the package contained Fluimucil, which is legal in sport and "administered on a regular basis".
A judge in the north-western Mexican state of Sonora has ordered the arrest of 22 people in connection with a deadly fire in a nursery in 2009.
[NEXT_CONCEPT]
The British Cycling coach who couriered a 'mystery' package for Sir Bradley Wiggins has been invited by MPs to give evidence at a doping inquiry.