Mahinda Rajapaksa had to cancel his helicopter trip from Polonnaruwa in the east to the badly affected coastal city of Batticaloa 120km (75 miles) away.
The downpour is continuing after two weeks of rain in the centre and east.
The floods have inundated farmland and destroyed rice fields.
Emergency
The eastern cities of Ampara and Batticaloa have been worst affected by the deluge, which has left some stretches of railway line under nearly a metre of water.
Officials in Ampara say the rainfall there since Saturday has been the highest ever recorded in such a short time.
A number of big reservoirs have burst their banks, destroying paddy fields in a major rice-growing area.
People in some areas have told the BBC they have seen no sign of aid agencies or government relief, and that some people in makeshift camps have been missing out on meals.
The air force has helped evacuate people and drop food supplies to some cut-off communities.
The government has made an emergency appeal for ordinary people's help in sending dry rations, mattresses and bottled water.
Clean water and food supplies have been sent by official and international agencies to the worst-hit areas.
But the deputy disaster management minister Duleep Wijesekara said some places, such as Mutur, have been difficult to reach.
"I boarded a high-speed navy boat to get there [to Mutur], but due to the huge waves we had to turn back after sailing for about 15km. After that we had to send food in by air," he added.
The floods bring a risk of disease, including the mosquito-borne dengue fever, which even in normal times is a severe problem in the country.
