Teams of National Disaster Response Force (NDRF), Navy, Air Force, Army, Railways and state administration rescued all the passengers, he tweeted. The home minister also said the central government is closely monitoring the entire operation. "Kudos to the rescue teams for their exemplary effort," he said.
Central Railway (CR) officials said all the passengers, including nine pregnant women, were rescued by 3 pm.
The train had left Mumbai for Kolhapur on Friday night, but could not travel beyond Vangani, where it reached in the wee hours Saturday.
Talking to PTI, chief spokesperson of the CR Sunil Udasi said all 1,050 passengers were taken to a safe spot.
"A special train with 19 coaches will leave from Kalyan to Kolhapur with the affected passengers of the Mahalaxmi Express," Udasi said.
Officials involved in the rescue operation said the nine pregnant women and a one-month-old baby girl were also safe.
Union Minister of State for Home Affairs Nityanand Rai spoke to Chief Minister Devendra Fadnavis and assured him that all central assistance will be provided to the state, the Chief Minister's Office (CMO) said in tweet earlier.
As rain continued to lash the coastal districts of Maharashtra, many towns were practically underwater since early on Saturday as flooding local rivers and other water bodies overflowed into residential areas.
While the city's lifeline, the suburban trains in Mumbai functioned with delays of 15-20 minutes on Western Railway and CR, the latter had to cancel services between Karjat-Kalyan (in Thane) owing to floods and waterlogging on the tracks since Friday.
Though the country's commercial capital continued to get intermittent showers and rain, the worst-hit were Thane and Ratnagiri with towns of Ulhasnagar, Murbad, Badlapur, Tiwala, Vangani, Khed, Mangaon, Mandangad, Chiplun and surroundings practically submerged.
In Mumbai, Minister of Education Ashish Shelar authorized school and college principals to declare a holiday to ensure students are not inconvenienced if heavy rain continued.