Opposition MPs have called on the home secretary to resign after documents suggested she misled Parliament over her decision to house asylum seekers at Kent's controversial Napier Barracks.
Health officials, inspectors and a High Court judge have examined concerns dormitory use led to a Covid outbreak.
Priti Patel said in February that "use of the accommodation was all based on Public Health England (PHE) advice".
However, a Home Office email said PHE advice viewed dorms as unsuitable.
Amid calls in the Commons for Ms Patel to resign, SNP MP Joanna Cherry said: "What she said - that the department had previously followed public health guidance regarding Napier Barracks in every single way - was simply not factually correct."
She asked: "Why isn't the home secretary tendering her resignation as Amber Rudd (the former home secretary) had the grace and decency to do?"
Home Office minister Chris Philp said the department followed PHE guidelines "where possible".
A Home Office email from last September said: "Public health advice is just that - we don't have to follow it, but should we choose not to and then have an outbreak of Covid, the fallout would be significant."
It said: "Their advice is that dormitories are not suitable."
Documents published by the Home Affairs Committee showed how the Home Office detailed specifications in September and said "dormitories which can be adapted to be Covid-19 compliant are acceptable".
However, a note from a PHE official at the time said: "I don't know how dormitories can be Covid-compliant."
Three months later, further PHE guidance sent to the Home Office said: "All guests (asylum seekers in Home Office accommodation) should be treated as potentially infectious. They should have individual rooms with en-suite to avoid need to leave the room."
But in February, Ms Patel told MPs that PHE and local authorities gave guidance which her department had been following "in every single way".
Following questions from the BBC, the Home Office provided further background information on why the home secretary told MPs she was following PHE guidance "in every single way" when using dormitories at Napier Barracks.
"While the advice to officials from PHE was that dormitory style accommodation was not suitable," a spokesman confirms, "it also set out how congregate residential settings should be used if other accommodation is not available".
"We believed we were taking reasonable steps to give effect to the PHE advice as to the steps that should be taken to make dormitory accommodation as safe as possible."
The Home Office also states that throughout the setup and operation of the site, it has engaged with health officials to ensure it is fully aware of the most thorough and up-to-date advice and continues to make improvements to ensure the safety of those in asylum accommodation.
In the High Court in April, a witness statement by a senior Home Office official said: "Health agencies continue to have serious reservations about use of the site."
In the statement, Philomena Creffield quoted an unnamed health official and said "she/he has not been provided with evidence that Napier now provides a Covid-safe environment".
The official was said to have warned the Home Office "that the accommodation and configuration of Napier is not in line with the guidance and that another outbreak is inevitable".
Ms Creffield's statement accepted "congregate or communal settings give rise to an increased risk of transmission of Covid-19" but said, rather than close the accommodation, the Home Office was "working towards taking steps to improve our processes in terms of identifying and managing any outbreak".
Hundreds of men were housed at the disused barracks, as the Home Office faced an urgent need to accommodate asylum seekers arriving in boats across the Channel.
As the pandemic raged, up to 20 asylum seekers slept in dormitories with sheets separating beds.
In January, nearly 200 men caught Covid-19 in an outbreak at the site.
Last week, the High Court ruled the decision to house asylum seekers at Napier was unlawful, however the Home Office said the site would continue to operate.
Many residents were moved out in April, but lawyers said the number of residents has since gone back up to more than 265, with men sleeping in dormitories of up to 12.