Government figures showing a fall in the number of rough sleepers is hiding the real scale of the crisis, it has been claimed, with charities citing their own data that reveals a significant increase in the sum of vulnerable homeless people seeking help.

Those who work every day dealing with the issue of rough sleeping have called the estimates “not fit for purpose”, and criticised what they said was the high number of councils who did not even go outside to perform a count.

Official data released on Thursday shows that the number of people estimated to be sleeping rough on a single night in England fell by 411 (or 9%) from last year. There were 4,266 people estimated to be sleeping rough in autumn 2019.

The figure represents a second consecutive annual fall but is still up 141% on 2010. The government works out the number by taking a snapshot count on one night.

But Paul Noblet, head of public affairs at youth homelessness charity Centrepoint, said the statistics were “not fit for purpose”.

“It beggars belief that two in five of the local authorities participating in the snapshot survey didn’t even go outside to perform a count. Those experiencing homelessness deserve better than rough guesses,” he added.

Noblet said this winter alone, Centrepoint has estimated that 22,000 young people approached their local council for help because they were homeless or at risk.

“Until we recognise the true scale of the problem we won’t be able to fix it. Committing to ending rough sleeping by the end of this parliament is a welcome aim, but if we want to break the cycle of homelessness for good we also need to put in place sustained funding for hostels and affordable housing to give homeless people a long-term future,” he said.

Out of 317 local authorities who revealed their method of counting, just 25% conducted a count-based estimate of visible rough sleeping. A further 104 (33%) made an evidence-based estimate meeting including a spotlight count in specific areas. And 43% conducted an evidence-based estimate meeting with local partners, without going outside to perform a count.

According to official figures, which have been frequently questioned by the statistical regulator, the number of people estimated to be sleeping rough in London decreased for the first time in six years.

This comes despite separate figures – published by the Greater London authority – showing rough sleeping in London has hit a record high, with 8,855 people recorded as bedding down on the capital’s streets.

Concerns were echoed by the Glass Door homeless charity, which described the figures as a huge underestimate. It said the street count for the Royal Borough of Kensington and Chelsea took place after its shelters opened, for example, meaning none of the individuals staying in Glass Door shelters were included.

Lucy Abraham, chief operating officer for Glass Door, said: “These statistics grossly underestimate the true scale of homelessness. We know that many of the borough-coordinated street counts took place after Glass Door and many other charities had opened their shelter doors to rough sleepers for the winter.”

The charity said 700 individuals stayed in a Glass Door shelter and about 2,200 stayed in other church-based emergency shelters in London last winter. “Imagine what our communities would look like if all 2,900 people were on the streets instead,” said Abraham.

Evidence from Glass Door shows that the number of rough sleepers continues to grow. In the first 90 days of Glass Door shelters opening this winter, 1,407 individuals sought shelter, compared with 1,138 in the same period last winter – a rise of 24%. The charity said it had provided shelter to 752 individuals so far this winter.

The south-west of England was the only region where there was a notable increase in the number of people sleeping rough, according to government statistics. For all other regions the numbers were broadly similar or lower, with London and the West Midlands showing the biggest fall.

On the eve of the official release, figures obtained directly from councils using the Freedom of Information Act showed numbers almost five times higher than Whitehall estimates.

They related to people sleeping rough at least once during the year as opposed to the government’s one night snapshot.

The government’s snapshot for 2018 showed there were 45 rough sleepers in Oxford. But over the whole of 2019 the local council said 430 people were recorded as sleeping rough at least once, according to the data gathered by the BBC.

On Wednesday the Labour party called for the UK Statistics Authority to launch an investigation into the accuracy of government data, which it said were “seriously misleading”.

The government pledged an extra £236m to tackle rough sleeping, and said it would be urgently reviewing the issue. The new funding will go towards accommodation for up to 6,000 rough sleepers, and helping those at immediate risk of being on the streets.

Dame Louise Casey will lead the review into the issue to provide advice to both the prime minister and the housing secretary, Robert Jenrick, on what other action should be taken.

Polly Neate, chief executive of Shelter, said: “The prime minister rightly wants to end rough sleeping before the end of the parliament, but unless his government tackles the drought of genuinely affordable homes, homelessness isn’t going anywhere.”

Speaking before a visit to a homelessness charity on Thursday, Boris Johnson said: “It is simply unacceptable that we still have so many people sleeping on the streets, and I am absolutely determined to end rough sleeping once and for all.”

The controversy comes after some local authorities were accused of deliberately hiding the scale of the rough sleeping crisis by changing the way they compiled figures for 2018 following Guardian analysis.

Although official statistics do not attempt to record the number of people that sleep rough throughout the year, senior politicians have often presented the figures as a census of the country’s street population.