Asif Ali Zardari arrived to public backlash for not cutting short his tour of France and Britain while catastrophe unfolded in Pakistan.
The government's response to the country's worst flooding in 80 years has been criticised for being inadequate and slow.
The floods, triggered by unusually heavy monsoon rain over the upper Indus river basin over the past 10 days, has caused a trail of destruction from northern Pakistan to the south, killing more than 1,600 people.
Two million people are homeless and the UN estimate that around 14 million people have been affected.
The United Nations have issued an urgent appeal to generously support Pakistan at this difficult time.
The military has taken the lead in relief efforts while the government is under fire for what is perceived as a slow response.
The president was in the southern city of Karachi and was due in the capital later in the day, he is also expected to visit flood-hit areas.