Mr Yousaf was the highest-profile name to use the encrypted messaging service for government business in a year where his failure to improve NHS performance has seen calls for his resignation.
Officials did not release their messages following enquiries by The Scotsman, claiming the latter would require a search of all information relating to each minister and be too expensive.
Maree Todd, minister for public health, women’s health and sport, and Kevin Stewart, minister for mental wellbeing and social care, were included in the list.
Neil Gray, minister for culture, Europe and international development with special responsibility for Ukrainian refugees, who is viewed as a potential dark horse for the SNP leadership once Nicola Sturgeon steps down, is the other political minister who used WhatsApp for government business.
Dorothy Bain, the Lord Advocate, and Ruth Charteris, the Solicitor General, are the final two ministers listed as as using WhatsApp. It is not clear whether the messages covered legal advice.
The revelation comes almost a year after the Scottish Government claimed no ministers had used WhatsApp for government business across two months in 2021, a denial critics said now “stretched credibility to breaking point”.
Ministerial usage of personal messaging applications such as WhatsApp is controversial.
While it is relatively commonplace across politics in Scotland and the rest of the UK, established practice dictates any information relating to government business received or sent via WhatsApp message is passed on immediately or retained by the relevant policy area to record appropriately on the Government corporate record management system.
Earlier this year the High Court in England heard former prime minister Boris Johnson used his personal WhatsApp account to communicate “critical decisions”.
During the Greensill lobbying scandal, Nadhim Zahawi, chairman of the Conservatives, said he did not know how WhatsApp messages between David Cameron around Greensill Capital were deleted. Rishi Sunak, then chancellor, was also sent several WhatsApp messages by Mr Cameron on the topic.
The phone of another former prime minister, Liz Truss, was also alleged to have been hacked by overseas agents, with ministers warned the use of personal email and phones was creating “Wild West conditions”.
In Scotland, the ministerial code warns ministers to be “particularly mindful of the vulnerabilities” linked to mobile phone and IT systems, telling them to take “all reasonable steps” to “ensure the security of government information”. The code of conduct for IT states civil servants must “never send” sensitive information using external emails or “over the internet” outside Government systems.
Officials admitted the six ministers had used WhatsApp for government business between the start of this year and late October.
The names were not provided in response to a Freedom of Information request, but were released after the Government was contacted directly for comment.
Officials claimed WhatsApp messages or other personal business application messagesrecorded in the Government’s corporate records are most likely to appear as “text within an e-mail, word document, or other recognised digital tool”.
This, officials said, meant “all documents relating to the appropriate ministers” would have to be searched to disclose the WhatsApp messages, breaching the cost limit for Freedom of Information requests. This effectively means it is impossible for the public to scrutinise what is discussed by ministers over WhatsApp, even if it is on government business.
Ministers also admitted to deleting WhatsApp messages after passing it on to officials to record. Given the requirement for ministers to be pro-active in sharing WhatsApp messages, this rule provides ministers with an opportunity to conduct government business on WhatsApp, delete the messages, and for them to disappear from the record.
Craig Hoy, Scottish Conservative party chairman, said the use of WhatsApp would “only raise suspicions” about what “crucial” government business is being conducted over WhatsApp.
He said: “There are no guarantees that these murky messages are being recorded in the correct way or if they are potentially being deleted after a certain period of time.
“It is time for SNP ministers to come clean and be transparent about their use of WhatsApp, especially in relation to decisions taken by those at the heart of this secretive government.”
Neil Bibby, business manager for Scottish Labour, added: “These revelations raise yet more questions about the SNP’s shoddy record on transparency. This Government have long treated principle of open government with total contempt, choosing secrecy and cover-up at every opportunity.
"It is essential that any and all government correspondence is being properly recorded and no-one can use WhatsApp as a way to dodge scrutiny.”
Alex Cole-Hamilton, leader of the Scottish Liberal Democrats, said the prior claim that ministers did not use WhatsApp had “always stretched credibility to breaking point”. He said: "Now it seems that government business is conducted on WhatsApp, but they have no intention of telling anyone about it.
"There's no good reason why messages that relate to government business should be off limits to journalists and the public simply because they were not sent by email. Ministers should commit to providing a searchable record of all messages that relate to government business, regardless of the channel through which they are sent.
"It's time to beef up Scotland's laws on access to information to prevent those in power riding roughshod over the public's right to know."
A Scottish Government policy said records were filed “according to subject and policy area” and not by medium.
A statement said: “Records management policy states that information and records should be retained as long as they are required to support the Scottish Government in its business requirements and legal obligations.”