The Nepali government is under fire for blocking private initiatives bringing desperately needed assistance to remote areas, and allegedly obstructing the flow of relief to the country.

Suman Prasad Sharma, the Nepali finance secretary, on Saturday denied charges made by NGOs and top international officials that the government was levying import taxes on aid or had blocked consignments.

According to reports in local media, hundreds of tonnes of vital supplies have been stopped at the Indian border.

One report quoted a local customs official at the frontier saying he had no orders to allow the relief through untaxed.

On Friday, Nepal was reported to have exempted only tarpaulins and tents from import taxes, prompting UN resident representative Jamie McGoldrick to warn the government to loosen customs restrictions to deal with the increasing flow of relief material.

“They should not be using peacetime customs methodology,” he told said.

Sharma said the charges were unfounded.

Villagers carry sacks of World Food Program aid over a bridge in Baluwa, Gorkha district. Photograph: Diego Azubel/EPA

“We haven’t sent back anything, and there’s no duty to pay on anything. These charges are completely irresponsible and I refute them,” Sharma said.

The death toll in the disaster has now passed 7,000, with more than 15,000 injured. Hundreds of thousands of homeless, including many injured, have yet to be reached.

However, it is increasingly clear that, as part of a broader effort to centralise the relief effort, police are stopping trucks loaded with supplies by private well-wishers headed to badly hit areas.

Earlier this week, with international aid agencies facing massive logistic and bureaucratic difficulties, these small-scale local initiatives were reaching distant villages first.

“They are not suffering so they do not care. They are just out to get the foreign money for themselves,” said Rashmita Shastra, a healthworker in a village in Sindhulpalchowk district, 50 miles from Kathmandu, which had been due to receive a shipment of aid that was eventually blocked by authorities because it was “unofficial”.

The village, where seven people died and which has been almost entirely destroyed, has not yet been visited by any government official or politician, though one aid agency managed to distribute some tarpaulins and rice late last week.

Even villagers in accessible locations beside roads only 30 miles from Kathmandu told the Observer they had yet to be contacted.

Nepalese soldiers load relief aid from residents of Sikkim, India, at Kakarvitta on Saturday. Photograph: Diptendu Dutta/AFP/Getty Images

Hundreds of helicopter flights have also been paid for by private individuals, religious foundations or businesses. It is unclear whether these will be allowed to continue.

Officials said private initiatives would be permitted if they were coordinated with local administrators.

Aanand Mishra, who launched a civil society and business initiative called Operation Relief Nepal immediately after the earthquake, said a new directive from the government ordering all money from overseas transferred into accounts opened after the disaster to be paid into the government’s own relief fund, had badly hit aid deliveries.

His organisation, backed by the Nepalese federation of chambers of commerce, had raised $50,000 (£33,000), which had already been spent on assistance.

“We could raise so much more but no one overseas wants to just transfer money to the government, so none of my foreign friends can help,” Mishra said.

Officials have also been criticised for failing to prepare for the crisis or to properly coordinate aid in its aftermath. Protocol and bureaucratic turf fights have weakened the response, while Sushil Koirala, the 75-year-old prime minister, appears to be unable to cut through the administrative chaos.

Koralia was heckled by angry crowds in the streets of Kathmandu last week amid mounting anger across the country.

More than 130,000 houses were destroyed in the quake, according to the UN humanitarian office.

Almost nothing is known about the situation in the badly hit Langtang area, where some western trekkers are thought to be trapped.

Udda Prasad Batwai, the most senior local official in Langtang, said that 250 people are missing, including 100 foreigners.

“Whatever we have, we are distributing. We are all working together, local NGOs, international NGOs and the administration. But there are lot of people who we can’t get to with our resources so small,” Batwai said.

The UN has estimated the quake affected 8.1 million people, more than a quarter of Nepal’s population of 27.8 million.

Many mountain roads, often treacherous at the best of times, remain blocked by landslides, making it extremely difficult for supply trucks to get to the higher Himalayan foothills.

“We definitely need more helicopters,” Ertharin Cousin, executive director of the UN’s World Food Program, said.

Krishan Gyawali, top official of Sindhupalchowk district, said at least 300 people were still stranded at Tatopani, a bazaar town on Nepal’s border with Tibet.

Gyawali said the district had only received very little relief assistance from the central government.

“We haven’t been able to reach to every place in the district. People are angry with us but what can we do, whatever is possible we are doing our best,” he said.

However, police spokesman Kamal Jung Bam said that distribution of relief was now of “significantly larger scale” than earlier in the week.

“Helicopters and vehicles have been ferrying relief packages from Kathmandu towards many parts of the country, especially to the most affected villages,” he said.

US military aircraft and personnel were to arrive in Kathmandu on Saturday to help in relief operations. One of their tasks would be to deal with the growing piles of aid material.

Some of the relief material for survivors was being held up at the country’s only international airport because of customs bottlenecks, the United Nations said on Saturday.

Nepali government officials have said efforts to step up the pace of delivery of relief material to remote areas were frustrated by a shortage of supply trucks and drivers, many of whom had returned to their villages to help their families.

“Our granaries are full and we have ample food stock, but we are not able to transport supplies at a faster pace,” said Shrimani Raj Khanal, a manager at the Nepal Food Corp.

Army helicopters have air-dropped instant noodles and biscuits to remote communities but people need rice and other ingredients to cook a proper meal, he said.