An email from the Mayor’s chief of staff, Edward Lister, ordered deputy mayors and advisers to “support” his campaign but Mr Johnson said it was later withdrawn.
“The advice also makes clear that GLA officers can, when not at work, express personal opinions (which be contrary to the Mayor’s views),” said the email, which was published by the BBC.
“Whilst this is the formal position for you also, I would expect, given your roles, you either to advocate the Mayor’s position or otherwise not openly to contradict it.”
The note claimed there was a “fundamental difference” between elections and referendums that mean the authority, which is funded by Westminster and taxes to control London’s transport, policing, emergency planning and other areas, is allowed to take a public stance ahead of the vote.
"Boris is entitled, as Mayor, to adopt a public position on this issue and then, as with all other mayoral policies, to receive support from GLA officers in relation to that policy position,” the email, thought to have been sent on Friday, said.
“There are no parties and no candidates, and so you are all able to be involved in the campaign as you wish (but without using the Authority’s resources for your personal activities)."
What's the European Parliament ever done for us?
What's the European Parliament ever done for us?
1/5 A cap on the amount of hours an employer can make you work
The Working Time directive provides legal standards to ensure the health and safety of employees in Europe. Among the many rules are a working week of a maximum 48 hours, including overtime, a daily rest period of 11 hours in every 24, a break if a person works for six hours or more, and one day off in every seven. It also includes provisions for paid annual leave of at least four weeks every year
2/5 Helping the people of Britain to avoid smoking
In 2014 MEPs passed the Tobacco Products Directive strengthening existing rules on the manufacture, production and presentation of tobacco products. This includes things like reduced branding, restrictions on products containing flavoured tobacco, health warnings on cigarette packets and provisions for e-cigarettes to ensure they are safe
3/5 Helping you to make the right choices with your food
Thanks to the European Parliament, UK consumers have access to more information than ever about their food and drink. This includes amount of fat, and how much of it is saturated, carbohydrates, sugars, protein and so on. It also includes portion sizes and guideline daily amount information so people can make informed choices about their diet. All facts must be clear and easy to understand
4/5 Two year guarantees and 14-day returns policy for all products
Consumers across the EU have access to a number of rights, from things which are potentially very useful, to things which used to be annoying. For example, shoppers in the UK receive a two-year guarantee on all products, and a 14-day period to change their minds and return a purchase, these things are useful
www.PeopleImages.com-licence restrictions apply
5/5 Keeping your air nice and fresh (and safe)
Believe it or not, although the situation is improving, some areas of the UK have appalling air quality. A report by the Royal College of Physicians released on 23 February says 40,000 deaths are caused by outdoor air pollution in the UK every year. Air pollution is linked to a number of illnesses and conditions, from Asthma to diabetes and dementia. The report estimates the costs to British business and the health service add up to £20 billion every year
Mr Johnson faced an immediate backlash, with people immediately pointing to his criticisms of the campaign to stay in the EU which he has previously described as “project fear”.
He made the comment while criticising the suspension of John Longworth from his role as the director general of the British Chambers of Commerce after he backed Brexit.
Mr Johnson said on Tuesday that the advice had been withdrawn, apparently after he was alerted to the BBC's impending story on the matter on Monday evening.
“Nobody has been gagged, I was only made aware of this edict very late last night and it ceased to be operative as soon as I was made aware of it,” he said.
“All I can say is it obviously hasn't been operative because my advisory team take a very different view from me...it's a cock-up and not something I agree with”.
His official spokesperson previously confirmed the existence of the order, saying it was "in line with that issued by the GLA's statutory officers".
"The mayor is relaxed about any of his team of advisers in a personal capacity campaigning for or supporting either side in the EU referendum,” he added.
"He wants to see an open and inclusive debate and recognises that some of his advisors have differing views to those he holds.
"In his role as chief of staff, Ed Lister advised the team that as official mayoral policy is now to support the case for leaving the EU, they are requested to support that position when undertaking official city hall business."
Mr Johnson is among a group of high-profile Tories including Michael Gove who are campaigning for an exit, while the Prime Minister is leading the Government’s official position on the “stay” campaign ahead of the vote on 23 June.
Additional reporting by PAReuse content