Around 150 people have so far been rescued from some places in the district.
Cyclonic storm 'DAYE' hit the Odisha coast near Gopalpur early Friday causing heavy rain and Malkangiri district, which bore the brunt, was virtually cut off from the rest of the state.
Special Relief Commissioner (SRC) B P Sethi said no loss of life has been reported till 12 noon.
The SRC said, Malkangiri district was severely affected by the cyclonic storm and some people were left marooned in submerged areas, including Poteru.
Around 150 people have so far been rescued from some places in the district, the SRC said.
Immediate steps have been taken for distribution of relief materials in the affected areas and damage caused by the natural calamity was being ascertained, he added.
Rain water was flowing over major roads, submerging low-lying areas in the district that experienced a total rainfall of 1163.8 mm since Thursday, Malkangiri Collector Manish Agarwal said.
After reviewing the situation, Chief Minister Naveen Patnaik has directed the Malkangiri district administration to reach out to the affected people and extend all assistance to them, an official in the Chief Minister's Office (CMO) said.
Mr Patnaik also sanctioned gratuitous relief for seven days at Rs 60 per day per person and Rs 45 each for children below 12 years in the district, he said.
The cyclonic storm "DAYE" over northwest Bay of Bengal crossed south Odisha and adjoining Andhra Pradesh coast close to Gopalpur in the early hours of Friday, Director, Meteorological Centre, Bhubaneswar, H R Biswas said.
The cyclonic system then moved west-northwestward with a speed of 26 kmph and weakened into a deep depression and lay centred over south interior Odisha and its neighbourhood, about 65 km east-southeast of Titlagarh.
After making a landfall, the storm triggered heavy rainfall in several places in Malkangiri, Gajapati, Ganjam, Puri, Rayagada, Kalahandi, Koraput and Nabarangpur districts of the state, MeT officials said.
Malkangiri, which recorded an average rainfall of 166.25 mm since Thursday, witnessed severe waterlogging and disruption in road connectivity in many areas.
As major roads were submerged with rain water, connectivity with Jeypore, Chhattisgarh and Andhra Pradesh remained snapped, said an official.
Water level in the Balimela reservoir had also risen alarmingly, he said.
While rain water gushed into a health centre in Janbai, four persons who had been marooned in a forest nursery near Malkangiri since Thursday were rescued Friday, he said.
Incessant rainfall also left major rivers like Saleru, Saberi and Saptadhara in the district swollen, while power supply remained snapped.
Heavy rains also lashed nearby Koraput, Rayagada and Nabarangpur districts.
The MeT centre forecast heavy to very heavy rain in several places in Rayagada, Kalahandi, Koraput and Nabarangpur districts till Saturday.
Heavy to very heavy rain is also likely to occur at some places in Balangir, Bararh, Jharsuguda, Sambalpur, Sundargarh, Keonjhar and Mayurbhanj districts till Saturday morning, it said.
The impact of the cyclonic storm was also felt in Gajapati, Ganjam, Khordha, Nayagarh and Puri districts, while districts like Mayurbhanj, Balasore and Bhadrak were lashed by heavy downpour.
The state government has instructed officials in coastal districts and various departments to tackle any emergency situation, official sources said.
While the IMD had predicted damage to thatched hut, roads, crops and minor damage to power and communication lines in Gajapati, Ganjam, Khordha, Nayagarh and Puri districts at the time of landfall, the state government is in the process of assessing the damage, if any.
Taking the situation into account, the NDRF and the ODRAF have been deployed in different districts. One NDRF team each has been deployed in Kalahandi, Rayagada, Gajapati, Puri, Nayagarh and Kandhamal districts with 17 boats and other emergency equipment.