The Treasury is seeking to block museums and art galleries from topping up the salaries of staff who have been furloughed under the government’s coronavirus job retention scheme, the Guardian understands.

Officials in the Department for Culture, Media and Sport (DCMS) have been told that “arm’s length bodies” in the heritage sector, which receive some central funding, should hold on to any extra cash to deal with other cost pressures, instead of paying the 20% portion of staff salaries under the scheme.

It means that lower-paid workers in institutions such as the British Museum, Imperial War Museum, and the Victoria and Albert Museum, which have been badly affected by Covid-19, could receive just 80% of their pay – the portion pledged by the government.

The job retention scheme, which opened on Monday, allows employers to furlough workers and claim back four-fifths of their salaries from the Treasury.

When Rishi Sunak, the chancellor, announced the scheme, he said: “Of course, employers can top up salaries further if they choose to.”

But in an apparent contradiction of the chancellor’s statement, the Treasury has told culture department officials that staff at some “heritage” institutions should not top up salaries. Museums and galleries generate up to 70% of their own income.

Jo Stevens, the shadow culture secretary, called for an explanation, saying that low-paid workers had to be supported through the crisis. “The chancellor was very clear when announcing this scheme that employers would be free to top up wages to 100% and that’s the case no matter who the employer is. Government should urgently consider the impact of this on the lowest paid workers.”

The implications of the Treasury’s position were dire for many workers, union insiders said. A large percentage of museum staff earn living wage or a sum close to it.

Unions have said they will not accept the furloughing of workers on 80% of salaries and will urge members to reject it too. The job retention scheme requires agreement before staff can be furloughed.

Alan Leighton, national secretary of the union Prospect, said: “The government should be leading by example on topping up furloughed workers’ wages. Instead the Treasury is blocking some employers from doing so even where they are willing to fund this from their own income or reserves. This is unacceptable and will be strongly opposed by Prospect and other unions.

“This money will make almost no difference to government given the scale of expenditure on supporting the economy during the crisis, but it will mean the world to these workers who are some of the lowest paid in the public sector.

“Given that other arm’s length bodies seem to be able to top up salaries, it is extraordinary that heritage seems to have been singled out in this way by government.”

Other public bodies such as Transport for London are topping up the wages of furloughed workers. Staff at the National Museums of Scotland are also being furloughed with a top-up.

Civil servants who cannot work from home but whose jobs are not essential are also being paid 100% of their salaries.

More than 140,000 companies employing a total of about a million workers put in applications to the government’s job furlough scheme on its first day of operation. It is understood the price tag attached to the requests is about £1bn, a figure that is likely to rise significantly as more companies make their applications for help over the coming weeks.

A government spokesperson said: “The coronavirus job retention scheme is designed to protect businesses and jobs across the economy at this unprecedented time.

“We expect all decisions by public sector employers accessing the scheme to be taken on a value-for-money basis.

“It may be appropriate for a public sector employee’s pay to be topped up under the scheme, in some exceptional cases.”