Prime Minister Yousuf Raza Gilani and Foreign Minister Hina Rabbani Khar too were present at the meeting held at the presidency.
"Issues relating to security in the region were discussed during the meeting," an official statement said without giving details.
Sources said the leadership had discussed the situation in war-torn Afghanistan and the issue of reopening NATO supply routes, which were closed after a cross-border air strike by US aircraft killed 24 Pakistani soldiers in November last year.
Earlier in the day, Zardari and Gilani held a separate meeting and discussed the overall situation in Pakistan, including an energy shortage and law and order.
Gilani briefed the President about Pakistan's participation in the UN Conference on Sustainable Development in Brazil.
The premier told the President that Pakistan would be represented at the meet by Foreign Minister Khar and Climate Change Minister Rana Muhammad Farooq.
The premier also briefed the President about the energy situation in the country. The law and order situation in various parts of the country was discussed during the meeting, officials said.