The latest challenge will likely delay any attempt to return the members of Lev Tahor to Canada, where a court has ordered the children placed in the care of children's aid.
In an interview from Port-of-Spain, Attorney General Anand Ramlogan said the appeal was filed Friday with the chief immigration officer.
"We are now in the process of dealing with that appeal," Ramlogan told The Canadian Press.
"In the meantime, we anxiously await the position of the Canadian authorities."
Canadian justice authorities, however, have refused to discuss what steps they might be taking to get the group returned.
Given the pending weekend, it was unlikely the appeal would be held before next week at the earliest.
On Thursday, a court in Port-of-Spain dismissed an emergency challenge by the group against the decision by immigration authorities to deny them entry.
At least two Lev Tahor families left Canada for Guatemala this week, only to be stopped in Trinidad.
Early this week, an Ontario judge issued an emergency order that 14 Lev Tahor children be placed in the care of children's aid but police said all but two had left the country, some apparently via Mexico.
Sect members came to Canada in 2005 after their spiritual leader, Rabbi Shlomo Elbarnes, was granted refugee status here.
Child-welfare authorities in Quebec spent a year investigating issues related to hygiene, health, and allegations that the children weren't learning according to the provincial curriculum.
The group has denied all allegations of mistreatment.
Late last year, a Quebec court ordered that 14 Lev Tahor children be placed in foster care.
About 200 members — 114 of them children — left Ste-Agathe-des-Monts, Que., in the middle of the night, and moved to Chatham, Ont.
Last month, a judge found the move to Ontario was made to avoid the custody proceeding there and he ordered the children be turned over to child protection authorities in Quebec.
Denis Baraby, director of Quebec's youth protection services for the Laurentians region, said he has spoken with the province's ministry of justice and police about whether further legal action can be launched in effort to see the children returned to Quebec.
"You can't just disregard the justice system without facing consequences," he said.
He also expressed concern for the children still living with the sect in Chatham, saying child-welfare authorities in Quebec had planned to seek supervision of them as well before the community uprooted to Ontario.
"We started by taking these two families to court because we had finished our investigation, but it was clear we had another 20 or so we would have brought to the court's attention afterward," he said.
Those files have been sent to child services in Chatham, he said.
"I'm still worried about (the 14 children) and I hope we do something for those who are still in the community," he said.
Officially, the group in Trinidad is under the care of WestJet, which flew them there. WestJet is required to return them to Canada and will have to cover their costs in the interim.