"We try to be very honest with the refugees,"UNHCR's Indonesia representative Thomas Vargas told Fairfax Media."It is so important that you have a safe place to be and you do your best to try to prepare for your future because don't expect you are going to be resettled at all."
The project,funded by European Union Humanitarian Aid,encourages refugees to learn Indonesian,volunteer,participate in local cultural events and take advantage of educational opportunities for themselves and their children.
It says other options may be available,including returning to their home countries if safe to do so,and private family sponsorship for those with relatives in a third country.
"We will be putting up posters that has this information,we have already posted on our website,and this is the messaging that we are giving refugees to help them cope with the situation,"Mr Vargas said.
However the reality is that it is too dangerous for many refugees to return home and life is tough in Indonesia,which is not a signatory to the UN Refugee Convention.
It is illegal for refugees to work and education options are limited,with more than 90 per cent of refugee children not going to school.
Last year the UNHCR and partner agencies wereunable to provide basic support to 37 per cent of identified vulnerable individualsdue to limited human and financial resources,which it said further aggravated their vulnerabilities.
Khalil Payeez,a Hazara refugee from Pakistan,said one woman fainted after UNHCR representatives visited the Cisarua Refugee Learning Centre to warn that only the most vulnerable refugees – such as those who were sick or unaccompanied children – would be resettled.
"They said the waiting time in Indonesia could be 10 years,it could be 15 years or it could be forever for refugees,"Mr Payeez said."Maybe we will live here forever,but Indonesia will not give you citizenship."
He said the refugee who fainted had questioned how she could attend university if she was stuck in Indonesia for 15 years.
"This was the worst message. It was disappointing because you didn't get an answer that gives you hope or encouragement. It's always bad news that you hear."
Mr Payeez is the manager of the Cisarua Refugee Learning Centre,a school established and managed by refugees just outside of Jakarta,that is now the subject of a new filmThe Staging Post.
"It gives their life meaning,community and friendship,"says film maker Jolyon Hoff."It has been beautiful (to see) their growth as individuals. If they are going to be stuck there indefinitely,education has to be the solution."
The Cisarua Refugee Learning Centre,which has been running since 2014,teaches 122 children between 5 and 17 years and also offers afternoon English classes for women,many of whom are illiterate in their own language. It has a lengthy waiting list and has inspired eight other refugee schools in Indonesia.
The UNHCR's Mr Vargas said he was glad to see these initiatives but would like to see more refugee children attend public schools in Indonesia.
"It's great that the children are getting instruction and are learning and are not stopping their development,but the problem is they don't get any kind of accreditation,"he said.
Although refugee children theoretically have access to primary and secondary education in Indonesia,only about 50 children are enrolled in public schools.
Mr Vargas said obstacles included language barriers,a lack of willingness on behalf of parents to enrol their children because they saw their stay in Indonesia as temporary and a lack of availability of places.
"We have been trying to overcome some of these obstacles,"he said.
Non-profit organisation Dompet Dhuafa holds Indonesian classes for refugee children to prepare them for entering Indonesian schools.
Seven year old Sabrina from Ethiopia can already interpret for her mother when she pays the rent,goes to the hospital and shops at the market.
"We might be in Indonesia for a long time and it is very important to study Bahasa Indonesia as well as English,"says her mother,Fatia Mohammed.
"I hope she will graduate from here and go to an Indonesian school - she already plays with Indonesian children in her free time. I am really proud she speaks Bahasa."
But others are not so lucky. Saad Mohammed Hussein,also from Ethiopia,wept as she said her 17-year-old daughter could not attend classes provided by Dompet Dhuafa because they were too far away.
"She doesn't do anything,she is stressed and almost committed suicide,"Ms Hussein said."We have been here for three years and the life is really difficult."
Ms Hussein said she had fled torture and persecution in her homeland. All she sought,she said,was a peaceful country where her children could access education and she could work.
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"I am very concerned about the future of my daughter. Education is the key to success."I have never been to school and if my daughter ends up the same as me it is a lack of progress."