After landing on Saturday, Mr Trudeau was received by a junior agricultural minister and despite being in India for two days has not met with the Indian prime minsiter Narendra Modi.
The Canadian PM and his family were also only received by district officials when he visited the iconic Taj Mahal in Agra a day later on Sunday.
The Indian leader was also absent when Mr Trudeau visited his home state of Gujarat on Monday.
Diplomatic sources said by “downgrading” these subtle arrangements, Mr Modi’s Hindu nationalist Bharatiya Janata Party (BJP) government was “indicating” its displeasure over Mr Trudeau attending an event organised by Sikhs in Toronto last May.
The event sparked controversy in India after it emerged that posters and flags demanding the Sikh homeland of Khalistan were displayed.
In a running diplomatic battle India has accused Canadian administrations of backing these Sikh groups, known as Khalistani’s, who want independence in northern Punjab state.
Vivek Dehejia, a columnist and economist who splits his time between India and Canada also told the BBC: ”Yes, this is a major snub. The fact that a junior minister was sent to receive Mr Trudeau and his family is most definitely a snub.”
Sikh activists had also acquired political importance in Canada over the years which has also frayed relations.
Last year Captain Amarinder Singh, the chief minister of Punjab, had refused to meet Harjit Sajjan, the Canadian defence minister, during his visit to Punjab last April over claims the ethnic Sikh minister was a Khalistan sympathiser.
However, Mr Sajjan has rejected allegations that Canada was supporting Sikh militancy aimed at creating a separate Sikh state within the Indian Punjab.
The Canadian PM and Indian leader are due to meet in Delhi on February 23 where discussions between the two delegations are expected to include cooperation in the fields of civil nuclear, space and defence.
Meanwhile Mr Trudeau is expected to meet with Mr Singh on Wednesday.
The chief minister of Punjab tweeted: “Look forward to meeting Canadian prime minister Justin Trudeau in Amritsar on Wednesday.
“I’m hopeful that this meeting will help strengthen the close Indo-Canadian business ties as well as the deep-rooted people-to-people relations between our two countries.”
Canada is home to 4.68 million Sikhs, comprising 1.4 percent of its population and a small, but influential number of them had financially and politically backed the 15-year Sikh insurgency in northern Punjab state for an independent Khalistan.