More than two animals and plants a year are becoming extinct in England and hundreds more are severely threatened, a report published today reveals.

Natural England, the government's agency responsible for the countryside, said the biggest national study of threats to biodiversity found nearly 500 species that had died out in England, all but a dozen in the last two centuries.

The losses recorded compare with a natural rate of about one extinction every 20 years before humans dominated the planet, but are almost certainly an underestimate because of poor records of any but the "biggest, scariest" creatures before the 1800s.

The high rate at which species are being lost is set to continue. Almost 1,000 other species face "severe" threats from the same problems that drove their relatives extinct – hunting, pollution, development, poor land management, invasive species and, more recently, climate change – says the report, Lost life: England's lost and threatened species. This represents about a quarter of all species in the best-studied groups, including every reptile, dolphin and whale species, two-thirds of amphibians and one-third of butterflies and bumblebees. In total, the report records 55,000 known species in England.

"Each species has a role and, like the rivets in an aeroplane, the overall structure of our environment is weakened each time a single species is lost," said Helen Phillips, the agency's chief executive. "We seem to have endless capacity to get engaged about rainforests but this reminds us conservation begins at home."

Tom Tew, Natural England's chief scientist, called for a "step change" in conservation, including more "targeted" schemes to protect individual species, better safeguarding of protected areas and better management of land outside the protected areas, especially farmland.

"This report is not all doom and gloom, but we're losing species at an alarming rate and many of our species are seriously threatened," he said. "These species could the tip of the iceberg unless we take action."

Matt Shardlow, head of Buglife, said: "The report [confirms] we are in the midst of an extinction crisis and it is happening here in England under our very noses."

Dozens of scientists trawled records going back to the first century AD from official lists and books. They identified 492 species recorded in England that could no longer be found, all but 12 of which disappeared after 1800.

A further 943 species are listed under the UK's Biodiversity Action Plan (BAP) as plants and animals under threat. These include a number of species now extinct in many counties or regions of England. One statistic that shocked the experts was a study of nearly half of English counties, which showed one plant species going locally extinct every two years.

So widespread are the problems that some once prolific species are under threat, including the common toad, common frog, common skate and the corncrake. "They are not common any more," said Tew. "Our ancestors used to lie awake at night unable to sleep because of the noise of the corncrake."

Four of the species extinct in England also became extinct globally: the penguin-like great auk; Mitten's beardless moss; York groundsel, a weed only discovered in the 1970s; and the Ivell's sea anemone, last seen in a lagoon near Chichester.

Many more English animals and plants are also on the threatened list, including the whitebeam, a tree with young leaves like "white candles", said Tew: "That signals the start of spring; it can be found nowhere else in the world and has disappeared from much of England."

The remaining extinct and threatened species exist in other countries, though the agency warned that reintroducing species was not reliable because the threats still remained, and national or regional extinctions led to the loss of genetic diversity.

Last year Natural England also published a report highlighting the economic cost of not protecting natural ecosystem services such as clean air, clean water, productive soils for crops, carbon storage, flood defence and natural resilience to climate change.

Other benefits were beyond value, said Tew: "Lots of you, like me, feel the worse for not hearing the corncrake in the country, or the flash of a red squirrel. When we lose wildlife we lose something priceless, and that effects our quality of life."

The report calls for better conservation, especially following successful schemes to reintroduce or bolster populations such as the red kite and large blue butterfly.

Of the hundreds of species on the BAP list in the 1990s, seven have since become extinct but 45% are now stable or recovering. The government has also ordered a review of protected areas.

"Species loss is not inevitable; we can do something about it," added Tew. "But we need to think ambitiously if we're to meet the needs of this and future generations."

This week, Simon Stuart, who oversees the team of experts that declare species globally threatened and extinct, said humans were causing extinctions faster than new species could evolve for the first time since the dinosaurs disappeared.

Winners and losers

Going: Species facing "severe" threats in England

Red squirrel

Northern bluefin tuna

Natterjack toad

Common skate

Alpine foxtail

Kittiwake

Grey plover

Shrill carder bumblebee

Recovering: Recent conservation success stories

Pole cat

Large blue butterfly

Red kite

Ladybird spider

Pink meadowcap

Sand lizard

Pool frog

Bittern