Speaking to reporters here after holding a meeting with the key leaders of the ruling Maha Vikas Aghadi on the issue, Thackeray said that the assistance will be provided by Diwali.
Fadnavis said the three ruling parties in the state have many differences among them, but they are expert in getting away from their responsibilities.
Heavy rains and floods have claimed at least 48 lives in Maharashtra's Pune, Konkan and Aurangabad divisions while crops on lakhs of hectares have been damaged extensively.
Crops such as sugarcane, soyabean, vegetables, rice, pomegranate and cotton, spread over 57,000 hectares in Pune, Solapur, Satara and Sangli districts, have suffered damage.
In Pandharpur town, some 1,650 people were shifted to schools and buildings of religious institutions and are being provided food, Dhole said.
The NDRF has deployed two teams in Maharashtra, one each in Latur and Solapur to rescue people affected due to heavy rainfalls in the area.
Mumbai and neighbouring areas received intense spells of rain since Tuesday night, leaving many parts of the metropolis in waist deep water and disrupting rail and road traffic.
Maharashtra Minister Vijay Wadettiwar on Tuesday said students from flood-affected areas in the state can make a representation to the National Testing Agency through respective district collectors.
Besides Nagpur, several villages in neighbouring Gadchiroli district also witnessed flooding in some parts following heavy rains.
The India Meteorological Department (IMD) official added that an 'orange warning' (indicating heavy to very heavy rainfall) has been issued for the Vidarbha region for the next 48 hours.
Heavy to very heavy rainfall is likely to occur in Konkan and central Maharashtra over the next four to five days.
As the catchment areas of Radhanagari dam were receiving heavy showes, water was released, leading to a rise in the river's level, officials said.
Heavy rainfall in Krishna, Bhima, Tungabhadra basin areas of Maharashtra is expected to increase inflows to various dams and barrages in the neighbouring state.
Areas like Bandra and Mahalaxmi in the city received 201 mm and 129 mm rainfall, respectively, between 8.30 am on Wednesday and 6.30 am on Thursday.
The city has been witnessing heavy rains since Tuesday night, resulting in water logging in many areas.