The Prado will receive 30 percent less in state funding this year, the Reina Sofia has seen its budget slashed by 25 percent, and funds for the Thyssen-Bornemisza are a full third lower.
Spain's conservative government has slashed spending on culture by nearly 20 percent this year to €722 million euros ($940 million) as part of the steepest budget cuts in 40 years.
The cuts have frustrated Spain´s museum bosses.
"I think the cuts to museums are a strategic error," said Miguel Zugaza, director of the Prado, which raised its general admission price from €12 to €14 on February 8th.
"These institutions have shown a rare vitality and breaking this dynamic is a mistake," Zugaza told El Confidencial.
He added: "Beyond our educational role, we also have a huge economic responsibility. I don't know how we will come out of all this, but I think in terms of managing cultural assets, Spain has to play the leading role in Europe."
The man at the helm of the Prado said temporary exhibits would bear the brunt of the cuts as these ate up a large part of the budget.
But Zugaza dismissed the idea of "renting out" collections and talked instead about exchanges between museums.
Meanwhile, over the road at the Thyssen-Bornemisza, the museum's management are dealing with the budget cuts by developing various survival strategies.
"We have to maximize the museum's capacity to generate revenue and therefore what we have to do is get more visitors and ensure consumption increases," Evelio Acevedo, a former banking executive who was appointed a year ago as the museum's managing director, told media outlet AFP.
The cuts, combined with the loss of the Thyssen-Bornemisza's two main corporate sponsors last year, have put the museum "in a very complicated financial situation" but the success of its temporary visiting exhibitions last year helped it weather the storm, Acevedo said.
Museum suppliers are feeling the cuts too.
"Our bills are being paid late, especially in the case of regional institutions," Alejandro López, CEO of Stendhal told The Local.
Stendhal provides services including audio guides and ticketing solutions to many of Spain's museums.
López said that despite the crisis, visitor numbers at Spain's museums were rising very slightly. He said less locals were coming, but an increase in the numbers of foreign visitors was offsetting this.