Trudeau was accompanied by his cabinet ministers Harjit Sajjan, Navdeep Bains, Bardish Chagger, Kirsty Duncan, and Amarjeet Sohi.
He was escorted by Mallika Ahluwalia, the CEO and Curator of the museum, Union minister Hardeep Singh Puri, Minister of Local Government, Culture and Tourism Navjot Singh Sidhu, and Member of Parliament Gurjeet Singh Aujla.
Trudeau spent nearly 25 minutes at the museum.
He spent some time in the gallery of migration, hearing stories and looking at objects carried by people as they fled their homes and moved across the newly-drawn borders at the time of Independence.
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He spent the maximum time in the Gallery of Hope, which focuses on love and reconciliation. He left a note on the Tree of Hope writing that the museum is "a poignant reminder that dividing people is never the answer; we must learn to live together and love our differences."
Curator Ahluwalia said: "We are very grateful to Prime Minister Trudeau for visiting the Partition Museum. As Canada has a vibrant Punjabi community, the museum is very keen to record and include the stories of Punjabis settled there."
The Canadian prime minister is in India on a week-long visit. Earlier in the day, he paid obeisance at the Golden Temple in Amritsar.
The Partition Museum is the world's first museum dedicated to the partition of the Indian sub-continent in 1947. The museum is dedicated to all those millions impacted in the largest migration in human history and is a space of reconciliation.
It also aims to become a comprehensive archive on the Partition. The museum opened with a curtain raiser exhibition in October 2016 and opened all its galleries to the public on August 17, 2017.