The three girls were reported missing Sunday night at Maqsudan Police Station by their parents when they did not find them home after returning from work, an officer said.
The family of the migrant labourer had five children, said police.
The sisters were identified as Kanchan, 4, Shakti, 7, and Amrita, 9, they said.
All three bodies were sent for post mortem to ascertain the cause of the death, the officer said.
Shocking: Man kills daughter, ties body to motorcycle, drags through Amritsar village
Police said the matter unravelled when the father of the girls was shifting household items Monday and found the trunk heavier than usual.
When he opened the trunk, he found his three daughters inside, police said.
According to police, the father of the girls had recently received an ultimatum from his landlord to vacate the house over his drinking habit.
Investigation has been launched into the matter.
(With PTI inputs)
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