The meteorological department said that a deep depression in the Bay of Bengal was developing into a marginal cyclone and was set to hit the northern coast of Sri Lanka.
Following the warning, Sri Lanka started evacuating people from the coastal areas.
"We have decided to evacuate people living within 500 metres of the coast from Kuchchavelli in the east to Jaffna in the north," Lal Sarath Kumara, a deputy director of the Disaster Management Centre said.
Sri Lanka Red Cross said the mini cyclone may hit the north after midnight tonight.
Most parts of the country were lashed by heavy rains today and the disaster management centre said that over 4,000 people had been marooned in the northern district of Mullaithivu.
The southern district of Galle recorded the highest rain fall of near 140 mm with most of the roads in the districts rendered impassable.