It is a day of radically mixed fortunes for the arts in England, as organisations up and down the country receive news of their funding levels from Arts Council England (ACE).

In all, 638 organisations who applied for funding were disappointed as the crucial letters flooded into email inboxes this morning. Of those, 206 were formerly funded regularly by ACE.

Alan Davey, chief executive of the organisation, talked of "agonising and painful decisions" and "good organisations we have not been able to fund". He said there had been a "clear intellectual framework" for the decisions and a "transparent process".

But 110 new arts organisations were brought into the ACE portfolio for the first time, among them innovative young theatre organisations including HighTide Festival Theatre, Birmingham's live art Fierce festival and the much larger Manchester International Festival.

ACE, which received a 29.6% cut in its grant-in-aid from the government, passed on cuts of 15% to the arts as a whole, but it promised not to "salami slice", giving equal pain to all. This meant there were big winners – and big losers – as the funding decisions were announced.

Exeter Northcott theatre and Derby theatre lost their funding totally. So did the organisation that exists to help arts organisations raise funds, Arts and Business. Also disappointed this morning were Shared Experience theatre company and the Riverside Studios in London.

The Almeida theatre in London took a surprise hit of 39% in real terms while its neighbour a few miles east, the Arcola theatre, saw its grant up by 82.1%. Punchdrunk, which has become famous for its immersive theatrical experiences in unusual spaces, had a hefty rise of 141%.

The large national organisations, such as the National Theatre, the Royal Opera House and the Royal Shakespeare Company, all received cuts, in real terms, of 15% over the period 2012-15. English National Opera had a slightly smaller real-terms cut of 11%.

Tony Hall, chief executive of the Royal Opera House, said: "It is fair that the big organisations take what cut they can to allow others to survive and do great things. Alan Davey has come up with some wise judgments."

In the field of visual arts, the Institute of Contemporary Arts, which has struggled financially in recent years, took a heavy 42% cut, but Davey called thenew grant of £900,000 a year "a good amount of money … Putting this amount of money in is a vote of confidence in their future."

There were uplifts for galleries, such as 107% for the South London Gallery, currently enjoying a successful period, and increases for a trio of new galleries about to open – FirstSite in Colchester (up 16.8%), the Hepworth in Wakefield (up 7.7%) and Turner Contemporary in Margate (up 9.8%). Mima, in Middlesbrough, was a significant winner, with an upswing of 143.8%.

The country's symphony orchestras received a standard 11% cut in real terms, but Cambridge's Britten Sinfonia was rewarded for innovative touring work with an 11.8% increase; and Tête à Tête opera, which creates small-scale work in innovative spaces, became part of the portfolio for the first time, as did the Academy of Ancient Music.

Arts leaders spoke out against the cuts from central government. Tim Etchells, artistic director of the theatre company Forced Entertainment, welcomed his standstill grant, but said: "We feel that the government cuts – to the arts and to other vital areas of social provision – are both destructive and ideologically motivated. Cuts for the arts are particularly shortsighted given that the recent commitment to funding and development has made British culture the envy of the world and an industry which enjoys a sizable return on investment."

Tom Morris, artistic director of Old Vic, also received a standstill grant. "However," he said, "many organisations and cities have not been so fortunate. It would be easy to blame Arts Council England, but this is not their fault. They have been set a riddle to which there is no fair solution."

Ivan Lewis, the shadow culture secretary, said: "The contention that the cuts will not affect frontline provision of the arts have been blown out of the water. Half of those who applied received no funding. Arts Council England has tried to do its job in good faith … but taken together with cuts to local authorities and to higher education, the picture is not good."