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The Aral Sea catastrophe is one of Ban's top concerns on his six-day trip through the region and he is calling on the countries' leaders to set aside rivalries to cooperate on repairing some of the damage.
"I urge all the leaders ... to sit down together and try to find the solutions," he said, promising United Nations support.
However, cooperation is hampered by disagreements over who has rights to scarce water and how it should be used.
In a presentation to Ban before his flyover, Uzbek officials complained that dam projects in Tajikistan will severely reduce the amount of water flowing into Uzbekistan. Impoverished Tajikistan sees the hydroelectric projects as potential key revenue earners.
Competition for water could become increasingly heated as global warming and rising populations further reduce the amount of water available per capita.
Water problems also could brew further dissatisfaction among civilians already troubled by poverty and repressive governments; some observers fear that could feed growing Islamist sentiment in the region.
Ban also is taking on the region's frequently poor human rights conditions.
That is likely to be an especially tense issue when he meets Monday with Uzbek President Islam Karimov, who has led the country since the 1991 Soviet collapse and imposed severe pressure on opposition and civil rights activists.
The meeting comes less than two weeks after the U.N. Human Rights Committee issued a report criticizing Uzbekistan, including calling for fuller investigation of the brutal suppression of a 2005 uprising in the city of Andijan. Opposition and rights groups claim that hundreds were killed, but authorities insist the reports are exaggerated and angrily reject any criticism.