He said he had asked the Minister of State for Home Kiren Rijiju to personally supervise the rescue and relief operations and facilitate all possible help needed.
PM Modi said he had spoken to Arunachal Pradesh Chief Minister Pema Khandu and officials, both in Delhi and the states, on the flood situation.
Five persons were killed and nine went missing yesterday as a massive landslide triggered by incessant rains hit eight dwellings in Arunachal Pradesh's Papum Pare district.
"I am anguished by the situation arising due to floods in various parts of the Northeast. I share the pain of all those affected by floods," PM Modi tweeted.
"The entire nation stands with the people of Northeast during this time. Centre assures all possible help to normalise the situation," he added in another tweet.
In Assam, the flood situation deteriorated further yesterday, with six more people losing their lives and over 15 lakh people across 23 districts affected by the deluge.
With this, the toll in this year's flood related cases has gone up to 39, including eight in Guwahati, an Assam State Disaster Management Authority (ASDMA) report said.