The adverse content was noticed by the management of printing press when the magazine was brought in for printing.
A photo and an article portraying negative remarks over Modi was noticed by the press management and they denied to hand over the printed copies to the students.
The press management stood with their decision despite the protest from the CPM's student's wing Students Federation of India (SFI).
The magazine titled 'Puram Modi" was sponsored by the volunteers of SFI in Maharaja's Technical Institute.
Talking to PTI, owner of press James said, "The students came to us with a request to urgently print 300 copies of the college magazine for the year 2014.The article on Modi was noticed when the copies were being packed."
He refused to give the magazine copies to the students. The students asked him for compensation, to which he likely agreed.
In the meanwhile the college authorities said that the institution has nothing to do with the magazine and the fund for the magazine was raised among the students itself.
They also added that they have denied permission for the publication of magazine last year itself.
The police authorities are looking into the matter.
This is not for the first time that college magazine has created ripples of controversy in Kerala.
A case has been registered against the Principal and 11 students of Sree Krishna College at Guruvayur on June 16, 2014 when their college magazine contained obnoxious remarks on Modi.
In another case, Principal and six students of Government Polytechnique at Kunnamkulam was arrested for placing Modi's photograph in the college magazine along with Adolf Hitler, George Bush and sandalwood smuggler Veerapan.