A "serious allegation" concerning the "joint cremation of babies and adults" has been made about Aberdeen's Hazlehead Crematorium.
New council chief executive Angela Scott said the findings of an earlier independent audit would now have to be reconsidered.
It comes amid scrutiny of crematoria across Scotland and the issue of baby ashes.
The council apologised for the "further uncertainty".
A lawyer representing affected families described the latest allegations as "absolutely appalling."
In a statement, the council chief executive said: "Aberdeen City Council has endeavoured to be open and transparent about its own procedures at Hazlehead Crematorium.
"I have received a serious allegation regarding practices at Hazlehead Crematorium.
"The allegation relates to the joint cremation of babies and adults.
"In light of the allegation I now have to reconsider the findings of our independent audit which were published last year and I have advised Lord Bonomy's Infant Cremation Commission of this development."
She added: "I fully understand that public interest in this matter will be very high. I will, of course, share relevant information once I have it.
"On behalf of Aberdeen City Council, I want to take this opportunity to apologise for the further uncertainty that today's announcement creates.
"I also want to take the opportunity to reassure members of the public that they will continue to receive a kind and caring service at Hazlehead Crematorium.
"I would ask anyone with any concerns to contact us directly by completing the online form or calling 01224 522255."
Council leader Jenny Laing said: "The chief executive has indicated that she requires time to carry out a full and thorough investigation into this allegation.
"Until we are in possession of all the facts it would be inappropriate to comment further.
"This will understandably cause anguish among the community and be particularly difficult for bereaved families but we, as a council, will assist them in any way we can."
Police Scotland said it was not involved with the allegation.
Patrick Mcguire, from Thompsons Solicitors who are representing many of the families affected, said: "These latest allegations involving Hazlehead are absolutely appalling.
"The families I represent are almost broken by this news. Any suggestion that infants and adults have been cremated together must be rigorously investigated.
"At almost every stage Aberdeen City have tried to block or evade attempts by the parents to find out what happened to their babies remains. This has got to stop now. The council have to be completely open and honest and do the decent thing by these families by telling them the truth."
Paul Wells, one of parents involved, said: "To think that something like this could have happened to my son Scott, well it's the worst possible scenario. We have dreaded something like this, it's more than someone not doing their job properly."
A spokesman for the Scottish government described the latest allegation concerning Hazlehead as "concerning" and said it was right that it was now being "thoroughly investigated" by the council.
He added: "We are seeking reassurances from the council that these practices are no longer taking place at the crematorium."
Lord Bonomy, chairman of the Infant Cremation Commission, is expected to submit his recommendations on polices and practices at crematoriums across Scotland to the Scottish government later this week.
Aberdeen City Council revealed last month it had changed its processes for the cremation of children.
The council said that, since last November, ashes have been recovered in all cases and returned to the parents.
BBC Scotland revealed last year that no ashes had been offered to the families of infants cremated at Hazlehead Crematorium over a five-year period.