The books, titled 'Perak', 'Land of Cartoons in Malay' and '1 Funny Malaysia', were published late last year.
"All three publications have been banned for their contents that can influence the people to revolt against the leaders and government policies,", Malaysian Home Ministry said in a statement.
"The contents are not suitable and detrimental to public order," it added.
The works are mainly collections of comics by Zulkifli Anwar Ulhaque, known as Zunar, and other local cartoonists, questioning current events, such as the trial of opposition leader Anwar Ibrahim.
Zunar said that he was waiting for an official letter from the ministry, but vowed that he would not stop drawing.
"In Malaysia the government is like this. They won't allow alternative views. You can do cartoons, you can do whatever art work you want, but it must be in line with the government (view)," Zunar said.
"Drawing cartoons it's my social obligation ... I will highlight the issues that Malaysian cartoonist have failed to highlight so far. They can ban my books, they can ban my publications, but they can't ban my mind," he added.
Zunar has well over RM50,000 worth of reasons for demanding that the Home Ministry provide him with solid reasons for banning three of his books.
That sum, still rising, is what the government's move is costing Zunar from loss of sales.
"I want a proper explanation for the reasons given by the ministry, that the book could influence people to revolt against the leaders and government policies," he said.
"These are serious allegations that should be supported with strong evidence," he added.
However, Zunar remains unfazed by the government's action, saying that the Home Ministry's continued threats will not put a stop to his struggles.
Meanwhile, Malaysiakini plans to mount a court challenge against the Home Ministry's decision yesterday to ban 1Funny Malaysia, a cartoon book published by the independent news portal.
Malaysiakini chief executive officer Premesh Chandran described the action by Home Minister Hishammuddin Hussein to ban the book as “peculiar”.
"The cartoons in 1Funny Malaysia have already been published on the Malaysiakini website (in the Cartoonkini section). As far as we know, there has been no revolt against the government since they were uploaded," said Premesh.
He said Malaysiakini will therefore immediately file for a judicial review of the Home Ministry's decision.