"This is an unprecedented situation and we are doing the best we can under the circumstances. Please don't panic, we will reach you, I promise," he wrote on Twitter.
He said he has asked the cabinet secretary to direct the air force to use helicopters to evacuate people.
"I've spoken to the cabinet secretary heading the crisis management team in Delhi to direct air-lifting of boats to Srinagar urgently via NDMA and army," he said.
He added the evacuation was underway.
"...We are doing our best to reach all asap (as soon as possible). Please stay on the upper floors and wait for help to come," he said.
Over 100 people have died in floods in the state due to incessant rainfall during the week.
Union Home Minister Rajnath Singh took stock of the grim situation Saturday and Prime Minister Narendra Modi will be visiting the state Sunday.