Describing the train, which was introduced in 2006, as "Propaganda Express," Khan claimed at a gathering in Barmer that it was just a formality and had not achieved its intended purpose.
The train was "useless" for the people on the Indian side and there was no proper facility for those wanting to go to Pakistan as passengers, he alleged.
"There are no easy issuances of visas and no suitable stoppages from Jodhpur to Munabao, which makes the train just a compulsion to run," Khan claimed.
Khan was embroiled in controversy last year when the Union Home Ministry granted special permission to him to board the train at Munabao railway station in Barmer district, while the rules required passengers to come to Bhagat Ki Kothi in Jodhpur.
While this is the last station from where a passenger can board the train, Munabao is the last station in Indian territory near the international border.
At the gathering, Khan shared the dais with Chief Minister Ashok Gehlot, minister in-charge for the state, Mukul Wasnik, MP Harish Choudhary and some MLAs ahead of the visit of UPA Chairperson Sonia Gandhi.
The minister's statement comes at a time when the introduction of a goods train on the same route along with a bus is proposed to further cement relations between the two nations.