Conditions worsened on July 22 when more heavy rain and hail storms hit the country, signs environmentalists point to climate change.
"New climate framework"
The flash floods may have been exacerbated by deforestation that allowed water to rush down bare hillsides, said Francis Markus, from the International Red Cross.
These threats are among the issues Ban hopes to address with the leadership of this isolated country ahead of climate change talks later this year.
The secretary general said he will host a summit at the UN on the sidelines of the general assembly in September to galvanise support for a global deal in December in Copenhagen, Denmark, on "a fair, effective and scientifically ambitious new climate framework."
Negotiations to seal a climate change treaty at the meeting have been hampered by disagreements over targets for cuts in carbon emissions.
The planned treaty, due to take effect from 2013 as the successor to the Kyoto Protocol, will shape planetary action up to the middle of the century.
Ban was also due to meet Mongolian troops participating in international peacekeeping missions, UN officials said.
At a welcoming ceremony in the capital Ban praised the country's efforts in peacekeeping abroad.
Mongolia's defence ministry announced on Thursday it would send at least 150 soldiers to Afghanistan in its biggest contribution to the international coalition fighting Taliban fighters there.
The Afghan mission follows Mongolian peacekeeping operations in Iraq, Sierra Leone and other countries.
Ban will meet Tsakhiagiin Elbegdorj, the president, and Sanjaagiin Bayar, the prime minister, on Monday.