The workers were trapped for 17 days.
The Lhonak lake in Sikkim state burst its banks.
It comes after Canada's Justin Trudeau accused New Delhi of being linked to a Sikh separatist's murder.
Preliminary findings have pointed to signal failure as the likely cause of the collision.
At least 275 people died in the crash with more than 1000 injured.
"We do not know how many more bodies will come," a health worker said.
About 900 people have been injured.
Violence between the Kuki and Meitei ethnic groups started in Manipur started last week.
Media reports say the assailants had been posing as journalists.
