Shaziman Abu Mansor said the government welcomed blogging but not negative postings by anonymous bloggers.
Critics however have condemned the idea as "anti-IT" saying it violates the government's own widely-touted 'no-censorship' policy for internet content.
There are about 50,000 websites registered using the .my suffix for Malaysia, Shaziman said, allowing anyone to host websites with malicious content.
"It's like asking a person who wants to start writing a personal diary to register with the government"
Ahirudin Attan, Malaysian blogger
What is malicious and negative content was not specified in the newspaper report, but such terms are generally used in topics considered as sensitive including criticism of the government, and discussions on race and religion.
The government proposal comes as two Malaysian bloggers, Jeff Ooi and Ahirudin Attan, face a defamation suit filed by the government-controlled New Straits Times newspaper.
They allegedly posted libellous remarks in their blogs about the paper's editors and executives.
The defamation suit against Ooi, who runs Screenshots, and Ahirudin, who blogs on Rocky's Bru, is the first time Malaysian bloggers have been hauled before the country's courts.
While the government and parties from the ruling coalition control much of the country's traditional media, many of Malaysia's most popular blogs offer political commentaries that include scathing criticism of government policies.
"Instead of coming up with ways to inhibit blogging, these ministers should be educated to start blogging themselves"
Lim Kit Siang, opposition leader
Ooi criticised the proposal saying the government should be "very sure of its objective in formulating new policies and guidelines" for the internet.
"The last four years has seen roughly 20,000 blogs spring up in Malaysia, including those which could not be sustained," he told Al Jazeera.
"If they [the government] are super-cautious of blogs, they need to specify what type of blogs or bloggers who pose a threat to national security."
Both Ooi and Ahirudin said the government was unclear on the concept of blogging.
Ahirudin said the government was trying to control what Malaysians were writing online and to create fear among bloggers.
"I think Shaziman is making the proposal out of ignorance, a lack of understanding of what blogging is all about," he told Al Jazeera.
"It's like asking a person who wants to start writing a personal diary to register with the government."
He said Malaysian bloggers were planning to set up an alliance to engage the government in discussions about blogs and blogging.
Some politicians with their own blogs have criticised the government's suggestion but acknowledged there were elements in the blogging community looking to stir up trouble.
Shahrir Abdul Samad, member of parliament for the southern city of Johor Baru, said bloggers were generally aware of ethical issues and the responsibility for their content.
But some bloggers do post inflammatory remarks, he said. The problem was also about comments left by anonymous visitors to the blogs, added Shahrir.
Lim Kit Siang, parliamentary opposition leader, said Shaziman's proposal showed that the government was becoming increasingly anti-information technology.
"I think this is the wrong approach altogether," Lim, also a blogger, said.
"Instead of coming up with ways to inhibit blogging, these ministers should be educated to start blogging themselves to invite a more interactive, communicative style of government."