The self-proclaimed "greenest government ever" today delivered some of its most vicious spending cuts to the environment. The Department for Environment, Food and Rural Affairs (Defra) had its total budget cut by 30%, including the effect of inflation, considerably higher than the government average of 19%.

It means that Defra's budget will shrink from about £3bn this year by about £700m by the end of the four-year spending period, in 2015. As a result, the department and its delivery agencies, including the Environment Agency, which monitors pollution and protects against flooding, and Natural England, which helps look after the natural world, will shed 5,000-8,000 out of a total of 30,000 jobs.

Some £170m will be cut from in flood spending, and savings from cutting jobs, IT spending and other administration will grow to £174m by the final year of the spending review period. Other savings under consideration include selling off or giving away National Nature Reserves.

But Caroline Spelman, the environment secretary, rejected claims that the severity of the cuts made a mockery of the pledge by prime minister David Cameron. "That commitment to become the greenest government ever goes across all government departments," she said. "If you bring into the equation the green investment bank, the announcement by [the climate change department which] greens our households for the future, if you look at announcements on public transport... these are all ways together we're able to reduce our carbon footprint and give clear expression to our desire to be the greenest government ever."

Defra's biggest cuts in money terms are in resource spending for administration and front-line services, which will be reduced by 29%, from £2.3bn this year to £1.8bn in 2014-15 – the third highest reduction in percentage terms of any government department. Capital spending, mostly on flood defences, will drop from £600m this year to £400m each year. Added up over the four years of the spending review, the department and its agencies will spend £2bn less than it would have, not accounting for the effect of inflation.

While flooding spending appears to have been decided in advance (a total of £2bn over four years), and farm subsidies are mostly protected because they come from the European Union, conservation experts said there was concern that most of the remaining cuts would fall on policies and projects to protect the natural world.

The RSPB welcomed the decision to maintain or increase spending on environmental stewardship schemes for wildlife-friendly farming, and to boost the more-effective "higher level" version.

However, the department has already announced restructuring and reduction in staff at Natural England, its main biodiversity agency. Concern will also be heightened by ministers' response today when challenged as to where other budget cuts would fall. Spelman highlighted a current review of regulation of food and farming, which environment groups fear will lead to far less enforcement of rules against a sector responsible for widespread damage to biodiversity and water pollution.

"I don't think we'll know the full ramifications of this until after Christmas," said Mark Avery, the RSPB's conservation director. "It can't be good news that Defra seems pretty close to the bottom of the list when it comes to handing out money, but Spelman has done a good job in defending and increasing wildlife-friendly farming."

Although flood spending will be cut by 20-30%, to a total £2bn over the four years, Spelman said that was significantly less than the 50% proposed by the last Labour government. She also defended the Chancellor George Osborne's declaration, in his main speech, that this would lead to a "major improvement" in flood defences: "efficiency savings" in the last year by the Environment Agency meant that the lower amount of money would still lead to an additional 145,000 homes being protected by 2015, she said.

Despite repeated questioning, Spelman was not able to say how much the cull of quangos would save in spending.