The squatter holding center at Sundari Ghat in Kirtipur-10 was inundated after the Bagmati River overflowed due to incessant rainfall.
Floodwaters entered the holding center on Friday night, leaving it waterlogged until Saturday morning.
A joint security team rescued 54 of the 154 residents and relocated them to the Smriti Building on the Tribhuvan University premises.
Others sought shelter with relatives or moved to safer locations near the holding center.
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