It's fair to say there are often times when central and local government are barely on speaking terms, but rarely does this make front page news. And for the nation's press to be universally taking the side of councils is practically unheard of.

Yet, the fallout from the Government's decision to quietly change advice for people living in areas facing a surge in cases of the coronavirus variant first found in India has done just that. Even the Conservative-supporting Daily Telegraph labelled Team Boris Johnson's actions a ‘farce'.

Local government could be forgiven if it collectively experienced a warm glow of satisfaction after ministers quickly backtracked on the change in travel advice for people living in Bolton, Blackburn with Darwen, Kirklees, Bedford, Burnley, Leicester, Hounslow and North Tyneside. Not least because the councils concerned had not even been informed of the initial change to advice for their areas.

With accusations of the Government imposing new local lockdowns and confusion running wild, the decision of the eight councils to jointly defy the national advice left ministers with no choice but to retreat.

As the directors of public health in each of the councils stood behind a message that there were no travel restrictions in their areas and no local lockdowns, ministers watered down their position to advise the public in the affected areas to simply minimise travel.

The devil's advocate may argue that the Government's initial tightening of advice was merely common sense, given the surge in cases across the eight authorities. However, even the most ardent defender of the Government would have to admit the handling of the affair was a mess. And much of the mess was down to communications.

As the secretary of state for transport, Grant Shapps, took to the airwaves to admit the Government's communications could have been better, there was a delicious irony as Boris Johnson's former right-hand man and message-meister, Dominic Cummings, prepared to lay into his former boss for a chaotic response to the pandemic.

For Professor Maggie Rae, president of the Faculty of Public Health, messaging was at the heart of the problem.

‘We've lobbied for clear messaging from Government,' she said. ‘But messaging has not been consistent and it's been very confusing.

‘The public are telling us they are confused again and that is not going to help us build trust and help us respond to the pandemic, even more so in the areas of greatest need.'

If the Government's revised advice sowed the seeds of confusion among the public, the Department of Health and Social Care's decision to simultaneously announce funding for nine councils to pilot initiatives to enhance self-isolation rates will have left some local authorities scratching their head.

While some of the nine councils benefitting from the pilot funding are in the firing line of the variant first found in India, there are several which aren't. It could be argued that those authorities fighting the current surge should be top of the list for any available additional funding. The counter-argument is that the £12m pilot scheme is an entirely separate matter.

‘The pilot is different to the current situation,' said Iona Lidington, director of public health at Kingston LBC – one of the pilot's beneficiaries. ‘It is a pilot that was applied for months ago as part of the learning. It has got muddled with the announcement of these additional measures for areas that have got very high rates.

‘You need to separate the two things. This is a pilot to test a gap in data and fill that gap to prevent onward spread. And anything that prevents onward spread, as the data will show, will be helpful.'

Kingston's performance has been strong. The authority has consistently been high up the London league table for test and trace and self-isolation rates, something Ms Lidington puts down to a supportive approach.

‘The first call offering support, advice and help to self-isolate, rather than "we're here to find out all your contacts" has made a real difference,' said Ms Lidington. ‘They have welcomed the support and not felt abandoned.'

Kingston has, however, spotted a particular problem with tracing contacts admitted to hospital, so their share of the pilot cash – the result of a joint bid with the local hospital – will go on embedding council tracers in the hospital to try and plug this gap.

It is, of course, reasonable that the two issues should be viewed separately. Something which could easily have been achieved if the Government had placed some breathing space between them. The failure to do so, however, has only heightened the criticism.

‘I would question whether you need pilots,' said Prof Rae. ‘We've been dealing with this pandemic since 29 December 2019. What we know about people finding difficulty being able to come forward for testing and to isolate is quite simple – it's fear of unemployment and fear of not having money.

‘People are simply not able to do it for financial reasons and poverty. I don't think we need any more pilots to tell us that.'

Prof Rae argued that the funding handed out through the pilot scheme should have gone to every local authority, because every council is facing problems responding to COVID and is stretched for money.

‘Local authorities have spent billions on COVID that they will never see back,' she said. ‘For every pound invested in local government you'll get it back tenfold because of the community engagement.'

There has, however, been some good news for those authorities facing a surge in cases but not benefitting from the self-isolation pilot funding.

‘The Government has offered us a degree of flexibility over the payments of self-isolation grants,' said Hounslow LBC's director of public health Kelly O'Neill. ‘For a period of eight weeks we will be able to not require all the level of evidence previously required and be able to pay up to 80% of people's salaries for their period of isolation.'

The apparent last minute nature of this offer will do nothing to dispel the impression that Westminster and Whitehall haven't got a firm hand on the tiller.

This impression will be even more pronounced for Blackburn with Darwen Council, one of the authorities to have also suffered the impact of a recent computer glitch in the national test and trace system, delaying the tracing of hundreds of potential COVID-19 contacts.

‘There doesn't appear to be a plan,' said Ms O'Neill. ‘These variants are going to happen all the time. Having a Government plan that sets out how we are nationally going to deal with them, rather than defaulting to hiding something on a website on a Friday evening about restricting travel is something we have got to get past.'

For all the questions over whether the Government is in control, has got its communications in order and is right or wrong to be funding pilot schemes, the more worrying issue may be its attitude to local government.

‘I wonder if we are still trying to run things from the centre,' said Prof Rae. ‘All my experience says you need a clear line of sight between national, regional and local in a country the size of England.'

‘We are seeing inconsistent messaging and local authorities seem to be the last to know what's going on. The Government is responsible for the pandemic response, but we are here to assist and help. As an observer to the local government system, I'd say you do not treat your allies with that lack of respect.'

Self-isolation support pilots

• Blackburn, Darwen and Blackpool

• Yorkshire and the Humber

• Cheshire and Merseyside

• Somerset

• Peterborough, Fenland and South Holland

• Kingston

• Newham and Hackney

• Lancashire

• Greater Manchester