Many pupils returning to classrooms in January will need extra support to make up for months of disruption.
Parents and principals said some pupils had fallen behind and efforts were under way to rectify the situation.
Concerns were also raised about the long-term effects of online learning on pupils' mental health.
It comes as Abu Dhabi announced that all pupils can return to private school classrooms from January.
Pupils in years seven to nine – or from about the age of 11 to 14 – will be the last batch to return to face-to-face classes.
They have studied at home since schools closed in March to limit the spread of Covid-19.
Most others returned in a staggered plan designed to prevent further infections and protect public health.
“My daughter was failing every subject at the end of September, while prior to this she would score 85 per cent and above in every subject," said Jennifer.
The British mother of two said she was worried for her daughter, 12, who will return to year eight in January.
“Her teachers were writing to me and saying she was not engaging in class. What worries me most is that she is not getting the support she needs."
The Abu-Dhabi resident, who works full time, said she felt her child was overwhelmed by a heavy workload, comparable to a university student.
"This is unfair to a 12-year-old. There is a massive learning gap and she has lost all motivation."
Jennifer said schools needed co-ordinators for each year to check on children's performance.
“Schools are failing a lot of children if they do not do this,” she said.
The issue is not just a UAE one. The emergence of a learning gap brought on the Covid-19 pandemic has been noted by international education chiefs.
Andreas Schleicher, the most senior education official at the Organisation for Economic Co-operation and Development, said schools across the world need to show a "massive shift in productivity" to make up for months of disruption caused by the pandemic.
OECD, which is comprised of 37 developed nations, found up to 60 full school days were lost between the outbreak in February and mid-May.
In September, British researchers found the average child in England was about three months behind, in a survey of 2,200 schools.
Data from the United Nations shows the pandemic affected nearly 1.6 billion learners in more than 190 countries, while closure of educational institutions affected 94 per cent of the world’s pupil population.
But schools in the UAE are working hard to bring pupils back to speed.
"Has learning suffered a bit? Yes, it has," said Iain Colledge, principal at Raha International School in Abu Dhabi. "Have individuals struggled? Yes.
“Face-to-face learning is always the best solution."
Pupils in grades six to 10 – ages 11 to 16 – will return to Raha in January, while children in other grades were already back.
Raha has counsellors assessing work to ensure pupils do not fall behind and Mr Colledge said that, while some pupils preferred online learning, others had struggled.
"There undoubtedly has been a slowing down of learning. But we don’t have data to show the difference."
He said pupils had missed social interaction and studying alone had affected their mental and emotional health.
When pupils return, the school would look at organising orientation programmes.
“Pupil's mental health and well-being is our primary concern. Some of them have struggled with their mental health," said Mr Colledge.
"We want to make sure they are happy.”
Parents also said they struggled with keeping children motivated.
Nihal E, a 36-year-old, Egyptian stay-at-home mom, said her eldest son struggled in some subjects during online learning.
Her sons, aged 11 and 13, study at Al Yasmina Academy, a UK curriculum school in Abu Dhabi.
While her younger son has returned to school, her eldest is studying at home.
“When I heard the kids are going back I was happy and excited," she said.
“The online learning experience was a shock.
“Children will most definitely need special help to revise what they have learnt online.
"I think the school has done an amazing job with the resources but the children have not reached their full potential."