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.
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.
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.
Get Breaking news, live coverage, and Latest News from India and around the world on NDTV.com. Catch all the Live TV action on NDTV 24x7 and NDTV India. Like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.