Aberlour's Young Runaways Service has always claimed flagship status.

Originally set up with funding from the then Scottish Executive, it has also been backed by the Scottish Government and has helped hundreds of young runaways since 2001.

Its 10th anniversary was marked by a reception at the Scottish Parliament which included a video message from the then children's laureate author Julia Donaldson, MBE, praising the service and wishing it success.

At that ceremony, Ken Dunbar, Aberlour's chief executive, spoke of the continuing need for help for children who run away from home – and often towards danger.

"Young people in Scotland are still running away, and still need support from organisations like ourselves, so we must do more to help young people before they reach crisis point," he said. Aberlour says one in nine children will run away from home before their 16th birthday and one in six of those will be the victim of a physical or sexual assault during the time they are away.

However, giving evidence at a recent session of the public petition committee's inquiry into tackling child sexual exploitation in Scotland, Mr Dunbar spoke of the difficulty of getting local authorities and other agencies to use the refuge, even though the need is acute.

As of this week, the refuge – the only one of its kind in Scotland – and all the related services including outreach support and a helpline for children, are shut.

The decision came suddenly at the end of last month with staff given a scant two weeks' warning of the decision. Permanent workers were offered redundancy or the chance to move to other vacancies within Aberlour – the largest Scottish children's charity – while sessional workers were laid off.

Admissions to the refuge were stopped and children remaining in the service moved on.

In a statement, Aberlour said the Glasgow-based service had been pioneering and set up in response to the fact a young person in the UK runs away from home every five minutes. The charity says a large proportion of these children are fleeing from neglect, harm and sexual exploitation.

A spokesman said Aberlour had invested almost £1 million of its own charitable resources into the Young Runaways Service since it was originally launched in 2001 as Running Other Choices (ROC).

He said it had campaigned vigorously to maintain the service, but added: "Given the realities of the financial climate we must constantly review the best use of our funds in order to reach as many vulnerable young people in Scotland as possible.

"Regrettably, due to low occupancy, linked to poor referral levels to the runaways' refuge in recent times and despite the high number of young runaways in Scotland, it is with sadness that we [took] the decision to close this service from end June 2013 and we will begin a consultation with our staff team on that basis."

He said strenuous efforts had been made to secure a viable future for the project and the decisions was not taken lightly. "As Aberlour has developed considerable expertise in the very complex area of young runaways we aim to continue to influence government policy."

But influencing government policy in this area is a far cry from Aberlour's previous messages about the need for more not less emergency accommodation for young run-aways in the face of varying estimates that between 9000 and 12,000 young people in Scotland run away from home every year. At the petitions committee, Mr Dunbar called for councils to face a legal duty to provide refuge for runaway children.

One former staff member is so horrified by the vacuum left by the closure of a service she describes as "awesome" that she intends to campaign for a replacement and ultimately even establish a charity to run a new refuge.

Social worker Abby Wills is the former assistant service manager of the Young Runaways Service, but left her post to travel three years ago. Recently returned, she thought the service so important that she was happy to return as a sessional worker.

Now she has been laid off, but most workers are more concerned about the plight of young people than their jobs, she says.

She believes cash-strapped councils are unable or unwilling to pay for beds in the refuge, but is also critical of her former employer.

"This was business decision, not a welfare decision," she says. "A service such as this for young runaways will never break even at the point of delivery.

"Something has gone wrong – this is exactly the kind of area a charity should be operating in."

A former Childline counsellor, she is not reassured Aberlour's helpline now directs young runaways to call that service.

"When I was working at Childline there wasn't a refuge. I remember how desperate the situation was for young people who were terrified, running because things were so bad at home. But there was nothing for them, nowhere to go. Now we are returning to that situaiton."

Many others in the child protection sector have expressed dismay at the loss of the refuge and runaways services.

Shelter Scotland runs an advice project for young runaways in Tayside. But the Safe & Sound project for Young Runaways, funded by the Big Lottery Fund, does not provide accommodation. Richard McGilvray, manager of the project, said: "The closure of this service leaves a massive gap in the provision of emergency accommodation for many of Scotland's young runaways.

"For these young people emergency refuges do not only offer a roof over their heads, but protection from exploitation and a springboard from which to rebuild their lives.

"Today's runaways are tomorrow's young homeless people. If we are serious about preventing future homelessness then supporting young runaways with basics like a roof over their heads in their greatest time of need is essential."

The UK charity Railway Children has been a long-term funder of the Aberlour service, and also expressed concern, blaming the closure on a tough financial climate.

Railway Children's head of UK policy and public affairs, Andy McCullough, said: "The closure of Aberlour Young Runaways Service is a major body blow to meeting the needs of some of Scotland's most vulnerable children.

"The vital need for this service is clear. At a time when child protection services are becoming more and more stretched, the service continued to make a huge impact on the lives of children in crisis."

There have always been two concerns about young runaways – what they are running from and what they are running towards. The links between child sexual exploitation and other forms of abuse and runaways are clear, Ms Wills argues.

She said: "The Scottish Government talks about doing more for trafficked young people and exploited young people. What do they think is happening to runaway children?"

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