Around six lakh people have been housed in over 2000 relief camps in the two states.
A Kerala government update at 5 PM said 102 people lost their lives across the state in floods and landslides, triggered by the second spell of monsoon, since August 8.
Officials said though people have started shifting to their homes in many places, there are still 1,89,649 sheltered in 1,119 relief camps.
Relief operations are in full swing in flood-ravaged districts of Karnataka, where the toll has gone up to 61 with seven more bodies recovered on Wednesday, as the rains abated in some areas.
Rains, which abated on Monday, battered various parts of Kerala since Tuesday night with the Met office in its latest update forecasting more showers, including heavy rain in isolated places, in the next few days and warning fishermen not to venture into sea.
The Met department in its update for the next 24 hours from 6 pm on Wednesday said the monsoon has been vigorous in most places in the state.
Strong wind from southwesterly direction with speed reaching 45-55 kmph was likely along and off Kerala coast, it said.
A red alert (extremely heavy rains) had been issued for three northern districts of Malappuram, Kannur and Kozhikode, which bore the brunt of the rain fury and landslips last week.
Pathanamthitta district was put on high vigil due to torrential rains since last night.
A holiday was declared for educational institutions in 11 of the 14 districts in the state on Wednesday.
The government announced a flood compensation package with an immediate financial aid of up to Rs 10,000 each to all calamity-hit families which had suffered loss in the floods and landslips triggered by the second spell of monsoon.
After chairing a cabinet meeting, Chief Minister Pinarayi Vijayan said Rs 4 lakh compensation would be given to those whose houses had been fully damaged or had become uninhabitable and Rs 10 lakh to those who had lost their house as well as land.
Flood-hit families and fishermen would be given 35 kg free rice.
On Wednesday, a fisherman drowned and three others were rescued when their fishing craft capsized in nearby Vizhinjam.
Despite inclement weather, search operations continued at Kavalappara in Malappuram and Puthumala in Wayanad, where a series of landslips had wiped out two villages last week, to trace those who were suspected to have gone missing.
Mallapuram district accounted for most deaths with toll there rising to 42 on Wednesday and 29 people still missing, followed by Kozhikode (17), Wayanad (12 deaths, 7 missing), Kannur 9 and Thrissur 8.
One person was missing in Kottayam district.
As per a state government update, 11,286 houses have been partially damaged and 1,060 fully damaged.
In a touching gesture, a Latvian national, whose sister was raped and killed at nearby Kovalam last year, has expressed solidarity with the people of the state facing the monsoon fury and made a contribution to the Chief Minister's Distress Relief Fund.
Chief Minister Pinarayi Vijayan was all praise for Ilze Skromane and said her act was "unparallelled."
In neighbouring Karnataka, inflows into the reservoirs were steadily decreasing, and flood situation has improved in the affected districts of north, coastal and Malnad regions, where the rain fury had created mayhem in the past one week.
"Relief operations are in full swing and senior officers camping in the districts to oversee the relief operations," an official release said.
While 15 people are still classified as missing, nearly seven lakh people have been evacuated till date.
Damaged roads are being restored on war footing for movement of men and materials, it said, adding that stability of schools and anganwadis are being assessed by engineers in flood-affected areas.
Joint rescue team comprising Fire and Emergency, SDRF, NDRF and Army have evacuated 6.97 lakh people as on Wednesday.
As many as 1,096 relief camps are operational, where clean drinking water, food and other relief materials are being provided to 3,75,663 people housed in them.
According to the government, 103 taluks in 22 districts have been affected by floods and incessant rains in the past few days, resulting in loss of agriculture and horticulture crops on 4.69 lakh hectares and damaging 58,620 houses.
Meanwhile, the CM's Relief Fund has received Rs 4.09 crore donation towards flood relief.