More than 2m cases of malaria are expected in Pakistan in the coming months in the wake of the country's devastating floods, aid workers have warned.

Two months into the crisis, large areas remain submerged in southern Sindh province, creating stagnant pools of standing water that, combined with the heat, are powerful incubators of a disease spread by mosquitoes that breed and hatch in the pools.

More than 250,000 cases of suspected malaria, including some of the fatal falciparum strain, have been reported, according to the World Health Organisation.

Aid agency Plan International worries the figure will surpass 2m. "The most vulnerable are women and children," said its Pakistan director, Haider Yaqub.

The malaria threat is part of a wider health emergency, with more than 20 million people affected by the floods struggling to cope as the winter approaches.

Last night the UN reported 881,000 cases of diarrhoea, 840,000 cases of skin diseases and almost 1m cases of respiratory disorders. Dr Dana van Alphen of the WHO said: "There are no epidemics yet – it's not Goma in 1994. But we have to be very careful."

Increasing UK aid to £134m recently, the international development secretary, Andrew Mitchell, warned of extremely serious public health dangers.

The floods have devastated Pakistan's flimsy public health system. More than 500 clinics have been damaged, while the government estimates that 30,000 "lady health workers" – a programme that is the backbone of the community health system – have been made homeless.

Pregnant woman are a particular concern. An estimated 50,000 flood-affected woman will give birth in the coming month, 7,500 of whom will require surgery for pregnancy-related complications.

The floods have highlighted the poor health of many rural people even before the flood. Doctors with the Pakistani Medical Association found that almost all women in Sindh and Punjab are clinically anaemic – half of them seriously so.

Midwives at refugee camps in Karachi, housing about 50,000 people, say many women had never previously been seen by a trained doctor. Pakistan already has one of the world's highest rates of maternal mortality, with 276 deaths per 100,000 live births.

The UN has requested more than $2bn to meet the humanitarian crisis, its largest appeal ever; so far about one-third of that amount has been pledged or donated. "We desperately need donors… These people have lost so much, but they still could lose more," said Jane Cocking of Oxfam.

So far UN agencies have treated five million flood victims; however, the onset of winter may make it harder to reach the remaining stricken victims. Access to the most northerly areas, in the Hindu Kush, will soon be restricted. Meanwhile, in southern Sindh province continued flooding means wide swaths are accessible only by boat or helicopter.