Sadako Ogata, the first female head of the United Nations refugee agency, who has died aged 92, was frequently underestimated by those meeting her for the first time. It was a mistake few of them made a second time.

When Ogata took up the post at the headquarters of the United Nations High Commissioner for Refugees (UNHCR) in Geneva in February 1991, staff knew almost nothing about her. First impressions were that she was too quiet, too self-effacing, too timid. There were doubts about whether she was up to the challenge of running one of the world’s biggest humanitarian organisations.

The scepticism was partly because she was a woman, at a time when few occupied senior UN positions. And she was Japanese, from a culture unfamiliar to many of the staff. Moreover, in an organisation dominated by career bureaucrats and former political leaders and foreign ministers, she was from the academic world, a professor of politics and international affairs.

Within weeks, scepticism about Ogata disappeared on the cold mountains of northern Iraq. More than a million Kurds were fleeing the forces of Saddam Hussein in the aftermath of the Gulf war. She flew by helicopter into the mountains to hear, at first hand, accounts from the refugees trying to escape to Turkey or Iran. Here was a UNHCR chief who refused to be deskbound, one who asked the right questions, listened and followed up with action.

From Iraq she flew to Iran and Turkey to seek their cooperation, and succeeded. She was quietly spoken and courteous in negotiations but direct and persuasive. She made an impression on the Tehran Times, which described her – she stood at just under 5ft – as “the diminutive giant”.

Ogata is rightly remembered for having broken the gender barrier at a major UN agency. But just as important a part of her legacy is that she transformed UNHCR, expanding its role to help millions more refugees.

Facebook Twitter Pinterest Sadako Ogata in Afghanistan, 2002. She believed in meeting refugees on the ground and hearing from them first-hand. Photograph: Erik de Castro/Reuters

The present head of the organisation, Filippo Grandi, was one of its field officers in the Middle East when she took over, and eventually became her chief of staff. “She understood immediately she had to get off the pedestal and into the battle,” he said, “and she was always like that. She moved the UNHCR into the thick of it. In the Balkans. In Africa. The Rwandan genocide.”

She was born Sadako Nakamura in Tokyo, into a family connected to the political and diplomatic world. Her mother, Tsuneko Yoshizawa, was a granddaughter of a prime minister, and her father, Toyoichi Nakamura, a diplomat. Sadako was brought up a Roman Catholic, one of a tiny minority in Japan.

She spent her early years in the US, China and Hong Kong, and was back at school in Tokyo when the US firebombed the city in 1945. She graduated from the University of the Sacred Heart in Tokyo, and went on to study at Georgetown University, in Washington DC, and Berkeley, in California. While researching a dissertation in Tokyo, she met Shijuro Ogata, whom she married in 1960. He went on to become deputy governor of the Bank of Japan, while she became a professor at Sophia University in Tokyo.

The Japanese government, obliged to include at least one woman in the delegation it sent to the UN general assembly, invited Ogata to join the team going to New York in 1968. She went on to serve on various UN bodies.

She understood immediately she had to get off the pedestal and into the battle

In 1979 she had her first direct contact with refugees, when she led a Japanese government mission to help Cambodian refugees. “I recall the shock and sympathy I felt for the refugees as I walked through the Thai-Cambodian border,” she wrote in her autobiography, The Turbulent Decade (2005). She was involved with Cambodian fugitives again in 1990 and her work there so impressed the UNHCR that she was frontrunner when the top job became vacant later that year.

Ogata never made much of the fact she was the first female head of UNHCR. She did not allow herself to be patronised. Staff recall a couple of meetings at which someone would open with the phrase “You as a woman”. She would respond immediately with “Why me as a woman?”

The biggest change she made to the UNHCR came on her return to Geneva after her experience among the Kurdish refugees. She called together senior staff on a Saturday for a debrief. In the middle of it, almost casually, she announced unilaterally that in future UNHCR would help not only refugees crossing borders but also those displaced internally by conflict.

She demonstrated her independence again during the Balkans crisis. As usual she had been on the ground, walking in a flak jacket and helmet through the streets of besieged Sarajevo and other embattled enclaves. In February 1993, faced with obstruction of food supplies and other humanitarian aid, she banned all shipments to Bosnia. This led to reports of a clash with the UN secretary general Boutros Boutros-Ghali. Staff who were there at the time said this was untrue. Although she had not spoken to him directly before taking the decision, he fully supported her. Within days she won: those involved in the obstruction caved in and supplies resumed.

She was famously impatient. Staff were the first to see the danger signs, her fingers tapping the table when faced with politicians or militia leaders or government bureaucrats she knew were lying.

Always pressing for more funds for the organisation, she was personally austere and frugal. On her first day in office she found her desk lacked basics such as pens, blotting paper and trays. She slipped out to buy them herself.

She left UNHCR in 2000 to return to Japan, where she went on to head the Japan International Cooperation Agency, the government body responsible for aid to developing countries. She was a frequent critic of the Japanese government for failing to provide sanctuary for refugees from Syria and other conflicts.

Her husband died in 2014. She is survived by her son, Atsushi, and daughter, Akiko.

• Sadako Ogata, diplomat, born 16 September 1927; died 22 October 2019