The United Nations High Commission for Refugees (UNHCR) says it cannot process refugee papers any quicker.
It also said that some people may simply be looking for the $100 dollars that has been offered by the UN agency to those that register.
Hundreds of trucks, paid for by the UNHCR to carry these people back to Afghanistan, have parked together to provide temporary respite for people who are angry about being mistreated.
Many refugees say they are being humiliated while they wait in limbo with their family members. Many have been living this way for more than three weeks.
Gul Wali, an Afghan refugee, said: "We have to spend thousands of rupees to go to our homeland, which is almost impossible for us. Our conditions here are miserable."
Although many of these families have been living in Pakistan for generations, they are now ready to return.
Liaquat Banori, chairman for the society for human rights and prisoner aid, said that repatriation is not the problem, but the real issue is instability in their homeland.
|Conditions are dire for Afghan refugees in |
but those in Afghanistan could be worse
"The refugees face miserable conditions," he said.
"There's no employment, no security, lack of water and no real shelter.
"The situation these people face is due to a miscalculation of the Pakistan government and the international community.
"If these people go back they will face dire circumstances and could very well come back.
"Repatriation is not the problem. The people, the Afghans in Pakistan, are ready and willing to return home.
"But where should they go? ... It is not conducive for them to go back and live a peaceful life.
"So, if the government of Pakistan is taking the decisions to force them back to Afghanistan ... and they don't find any place to live, what is the reasoning behind the government's decision?"
"It is much better for them to stay here [Pakistan] until there is security, peace and economic incentives in their country."
An estimated three million Afghans have left Pakistan and returned home since 2002 making it the largest such operation in UNHCR's history.