The UN has warned that waste and debris left in the wake of the 8 October South Asia earthquake could become toxic and seriously endanger survivors' health.
Debris could pollute the water sources, the UN says
Pakistan's environment minister also said reforestation was essential to prevent more deadly landslides.
The environment concerns were voiced a day after international donors pledged $5.4bn to aid Pakistan's recovery.
On Sunday, aid agencies welcomed the pledges but warned livelihoods as well as infrastructure must be rebuilt.
Pakistan says the death toll from the quake stands at more than 73,000. About three million people were initially made homeless.
Another 1,400 died in Indian-administered Kashmir.
UN environment programme official, Shafqat Kakakhel, said on Sunday it was essential to manage properly the "unprecedented large quantities of debris and waste".
"Otherwise a lot of the waste can turn toxic, can degenerate into toxic material, thereby posing serious challenges to health," he said.
Mr Kakakhel said the waste included toxic medical waste, rubble and "aid waste" such as bottles and cardboard boxes.
These, along with leakages from pesticide and petrol stores, could contaminate the water sources.
Mr Kakakhel also warned the Pakistani government that it must prevent trees being cut down for reconstruction.
Otherwise, he said the country's "timber mafia" might pillage resources for profit.
The country's environment minister, Tahir Iqbal, said the government would supply liquefied petroleum gas (LPG) to reduce dependency on wood for energy.
Mr Iqbal said reforestation was an urgent need.
"It was the landslides which wiped villages off the face of the Earth," he said.
"Areas where there were forests, landslides did not occur. Where the forests were depleted, whole mountains have just vanished."
On Saturday at a conference in Islamabad, international donors exceeded the $5.2bn in aid Pakistan had been asking for.
A total of $3.5bn has been earmarked for rebuilding the local infrastructure and homes, the rest set aside for helping the worst affected get through the winter months.
Aid workers and victims on Sunday welcomed the pledges but said the focus should not only be on infrastructure.
The International Labour Organisation (ILO) says up to one million breadwinners lost their livelihood.
ILO recovery specialist, Antonio Cruciani, said projects should focus on labour-intensive work and that local hiring was essential to bring incomes back to communities.
One farmer who had come to Muzaffarabad for shelter, Rab Nawas, told the Associated Press he feared the money would go to the towns.
"Nobody is paying any attention to the people in the mountains. If this is not done, those people in the cities also will suffer, because they will have no meat, no milk, no eggs."