The CIA has carried out hundreds of missile strikes on suspected militants in northwest Pakistan since 2004 and the campaign is a major thorn in relations with the US.
Washington views the strikes as an important tool in the fight against Al-Qaeda and Taliban militants, but Islamabad condemns them as a violation of sovereignty and international law.
Ban addressed the controversial weapons in a speech at the National University of Science and Technology in Islamabad, where he opened a new building.
“As I have often and consistently said, the use of armed drones like any other weapon should be subject to long-standing international law, including international humanitarian law,” he said to applause from an audience mostly made up of soldiers.
“This is a very clear position of the United Nations. Every effort should be made to avoid mistakes and civilian casualties.”
The United States insists the drone strikes are legal and in May President Barack Obama laid out strict guidelines for their use.
Britain’s Bureau of Investigative Journalism says the US has carried out nearly 400 drone strikes in Pakistan since 2004, killing up to 3,500 people, including hundreds of civilians.
Ban arrived in Islamabad for a two-day visit amid high tensions between Pakistan and India over the disputed territory of Kashmir.
He will meet Pakistani President Asif Ali Zardari and Prime Minister Nawaz Sharif for talks as Pakistan and India trade accusations over clashes along the Line of Control, the de facto border monitored by UN observers that divides the disputed Himalayan territory.
Islamabad on Monday summoned India’s deputy ambassador to protest against what it called “unprovoked shelling” which killed one civilian.
India’s army accused Pakistan on Tuesday of firing across the border in Kashmir overnight, but did not report any casualties.
Despite the Kashmir tensions, the UN said Ban’s visit would focus on education efforts and he is due to meet students later on Tuesday.
“In line with Malala Day last month he will meet with students in Islamabad to discuss efforts to promote and expand quality education for all,” a UN statement said.
The day was declared in honour of Malala Yousafzai, a Pakistani teenager campaigning for girls’ education who survived a gunshot to the head from Taliban extremists in October 2012.
The 16-year-old gave a moving speech at the UN in New York last month in which she vowed to continue to work for gender equality in education.
Nearly half of all children in Pakistan and almost three quarters of young girls are not enrolled in primary school, according to UN and government statistics.
During Ban’s visit officials of Pakistan’s National Disaster Management Authority will brief him about the floods in the country, where annual monsoon rains from July to September bring misery to thousands and inundate towns and villages.
Monsoon rains triggering floods have killed 84 people across Pakistan and affected more than 80,000 others this month, and officials have warned of further downpours.
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