Oxfam has called for urgent measures to reunite lost child refugees with their families on the dangerous road through Serbia.
The British aid charity urged better co-operation between agencies helping the displaced as official reports showed the number of children travelling alone had increased.
Youngsters were sometimes separated while queuing for registration on entry to the Balkan state while others went missing in crowded camps which process thousands of people needing healthcare and other support within a few hours, refugee accounts suggested. Many were reunited along the route.
Oxfam's humanitarian programme manager in Serbia, Anna Sambo, said: "We urgently need better co-operation between various agencies working with refugees so that when a family loses a child on the road the alarm can be raised and the child found as quickly as possible.
"At the moment we are seeing increasing numbers of children travelling alone.
"The dangerous situation can be a trauma for the vulnerable children.
"We want to ensure a presence to support families, women and children because we don't want them to be alone on their journey."
A What's App social network has been established to communicate photographs and other details across Serbia and into neighbouring Croatia. Lost person meeting points have been established.
However, some identity documents have been lost or stolen along the road, migrants said, while taxi drivers preyed on the vulnerable with offers of illegal transport.
Some taxis bypassed official registration points, leaving passengers with extortionate bills for short journeys and having to waste more money on retracing their steps to rejoin the established route, aid workers for Oxfam said.
At Presevo's refugee one stop processing centre close to the Macedonian border the numbers increased dramatically after a strike by Greek ferry workers created a backlog.
Sometimes women and children were put in different queues from men, increasing the risk of separation, Ms Sambo said.
Better transport arrangements have been introduced in co-operation with neighbouring states, the charity's field staff acknowledged.
However, the risk of countries closing borders is ever present after Hungary built a 109-mile razor wire fence along its frontier with Serbia.
There have been no reports of people traffickers targeting children in Serbia, a local aid organisation combating the trade said.
However, some refugees claimed they were left waiting for up to 12 hours in a queue in crowded and unsanitary conditions, near a large roadside ditch filled with rubbish.
Two little boys were left standing in the middle of a busy street, with traffic dangerously close and crowds all around as their frightened parents searched for another child who had gone missing.
The remaining children became more agitated the longer their parents were away. With police help, the missing child was found.
Zachariah Kwirah, a machine worker aged 25 from Syria, sat cross-legged on a blanket on scrubby grass surrounding a service station which served as a muster point for buses close to another of Serbia's borders.
He had arrived in the country with two sisters, his mother-in-law and three babies.
After queuing for hours to register in Serbia, with only an egg for sustenance, he had gone to find food for his family.
"When I came back the police stopped me and I said 'please, please' and they let me in.
"It was very tough, you say you are not an animal, why were they doing this to us? It gave us the feeling of being animals."