Mountainous Sikkim state plunged into chaos on Wednesday as floods spurred by heavy rain and an avalanche killed at least 40 people.
It was one of the worst disasters in the region in 50 years, and dozens remained missing on Friday.
The first part of the system, a camera to monitor Lhonak Lake's level and weather instruments, were installed last month, officials involved in the project told Reuters.
If fully operational, the warning system could have given people more time to evacuate, scientists said.
One scientist said glacial early warning systems can typically give residents a few minutes to an hour of notice.
Floods spurred by heavy rain and an avalanche have killed at least 40 people in northeast India.
Details of the Lhonak Lake warning system have not previously been reported.
"It's quite absurd, really," said geoscientist Simon Allen of the University of Zurich who is involved with the project.
"The fact it happened just two weeks after our team was there was completely bad luck".
He said they planned to add a tripwire sensor that would trigger if the lake was about to burst.
That would typically be connected to an alert system or siren that would warn residents to immediately evacuate to higher ground.
"The Indian government was not prepared to do that this year, so it was being done as a two-step process," he said.
The monitoring devices were supposed to send data to authorities, but the camera lost power for an unknown reason in late September, according to a source at the Swiss embassy, which supported the project.
As climate change warms high mountain regions, many communities are facing dangerous glacial lake outburst floods.
Water from melted Himalayan glaciers can overfill lakes, including in India, causing them to burst.
Lakes holding water from melted glaciers can overfill after heavy rain and burst, sending torrents rushing down mountain valleys.
More than 200 such lakes now pose a very high hazard to Himalayan communities in India, Pakistan, China, Nepal and Bhutan, according to 2022 research.
In recent years, glacial flood early warning systems have been deployed in Nepal, Pakistan, and Bhutan.
The early warning systems at Lhonak Lake, and another at nearby Shako Cho in Sikkim, were to be among the first in India for glacial lake outburst floods, sources told Reuters.
Scientists have for years said the two lakes are at risk of outburst floods, but the design process and search for funding caused time to pass without progress.
India plans to install early warning systems at several other glacial lakes, said Kamal Kishore, a senior official at India's National Disaster Management Authority.
He did not answer further questions on the Lhonak project.
However, Farooq Azam, a glaciologist at the Indian Institute of Technology Indore, noted that even if the system had been in place, the potential benefits were not clear-cut.
"Such kind of events are so fast that even if we have some kind of early warning system ... we may only gain some minutes, maybe an hour," he said.
