A brain drain of bright young women is already taking place in Afghanistan before the 2014 handover that many fear will mean a reversal of advances in women's rights.

The lack of commitment by the Afghan government to equality and to tackling the high rates of ill-treatment of women in the home and in the workplace is raising real fears they will be at the bottom of the political agenda in the push for power after Nato forces leave the country.

Worsening security for civilians – casualties among ordinary Afghans have risen year on year for the last five years with 3,021 killed in 2011, and women are thought to be suffering disproportionately – has led to rising numbers of women and girls leaving education and the workforce and staying indoors, according to Guhramaana Kakar, a gender adviser to President Hamid Karzai.

Speaking to the Observer, Kakar said negotiations between the government and the Taliban and other insurgent groups were ignoring women's rights. A recent survey by charity ActionAid suggested 86% of Afghan women were fearful of a return to Taliban-style rule. One in five worried about the education of their daughters but 72% said their lives were better now than a decade ago.

"Women do want the progress that has been made over the past 10 years to continue, but they are being kept away from the political processes," Kakar said. "All Afghans, men and women, want a country without foreign troops, but I think the international community should be putting women on the agenda and making sure their security and freedoms are secured, directly and indirectly."

She criticised the recent Nato conference in Chicago for completely ignoring the issue. "Women are regularly harassed in the workplace, they are exploited and credit for their achievements taken by men, while also being targeted by insurgents for going to work or school. They suffer the worst in the security situation and, even at home, they are subjected to violence and abuse which is tacitly sanctioned by the courts and the government."

Kakar has been involved in peace negotiations with the Taliban and believes more women should be allowed into the political system. "We have many women in parliament but they are given very weak roles. We have very brave women who are gaining respect and in some cases are trusted more than the men to negotiate, because they are seen as having less political baggage.

"If more women were allowed into the provincial and peace councils, this would be a big show to the insurgents that they cannot reverse 10 years of women's advancements."

Growing levels of violence against women and a disregard by many courts for their legal protection has led to horrific stories of children being raped and then imprisoned for adultery, and schoolteachers being attacked for teaching girls. ActionAid's head of public affairs, Melanie Ward, said the security situation was an enormous threat to women. "Experience tells us that an increase in attacks on women is often an early warning sign that the Taliban is regaining control in an area."

"Security for women cannot be divorced from the wider security agenda in Afghanistan."

Selay Ghaffar, chief executive of the Kabul-based NGO Humanitarian Assistance for the Women and Children of Afghanistan, says many young women are leaving. "They see no future for themselves in Afghanistan so the bright ones are seeking scholarships or work abroad. We have had two schools for girls burned down near the capital in recent days, acid attacks on girls going to school, increasing stories of rape and of kidnap.

"Many NGOs who try to help women have been killed. Billions of dollars from international organisations have been poured into Afghanistan and ended up in the pockets of male politicians, while women are left to feel insecure in their own land. For those who cannot leave, it is sending them back into the home; many women are deciding to stop work.

"During the first few years after international troops entered the country a lot of things changed in Afghanistan," she said. "There was positive progress and change in the day-to-day lives of many Afghan women. Unfortunately, since 2007, things changed dramatically as insecurity has increased [and] discrimination against women at all levels has increased. Life has become more difficult for women but they are not willing to be pushed back into the box.

"Why should all the plans for the future of Afghanistan ignore half of its population?"