His questioning on Wednesday follows allegations earlier this week from a senior member of the ruling UMNO party that a posting on Malaysia Today had mocked Islam and threatened racial harmony.
A bulletin on the website said he was being questioned at a police station in central Kuala Lumpur.
Raja Petra is well-known for his critical comments of the government and discourses on Malay rights and Islam.
He has said he was only against the behaviour of some Muslims, and not Islam itself.
Malaysia Today, which promotes itself as an "independent news" source, also posts articles by other bloggers and is one of the country's most popular political discussion websites.
'Irresponsible media'
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"In the name of freedom, these websites allow the broadcast of slander, lies and swearing, the use of harsh, degrading language and racial slurs without regard for the reader or those concerned"
Najib Abdul Razak, Malaysian deputy prime minister
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On Tuesday Malaysia's de facto law minister, Mohd Nazri Aziz, warned that it was "time to act" against what the government considers to be irresponsible or inflamatory blogging.
Speaking in Malaysia's parliament he said preventive detention laws could be used against bloggers who raise issues the government considers as being sensitive to Malaysia's multi-ethnic, multi-religious population.
His comments were echoed by Najib Abdul Razak, the Malaysian deputy prime minister, who told a gathering of the Malaysian Press Institute on Tuesday evening that the government was deeply troubled by the growth of what he called "irresponsible" alternative media.
He said bloggers needed to exercise moderation in postings which discuss race and religion or risk official action.
Webmasters and web journalists, he said, are not exempted from Malaysian laws.
"In the name of freedom, these websites allow the broadcast of slander, lies and swearing, the use of harsh, degrading language and racial slurs without regard for the reader or those concerned," the New Straits Times quoted him as saying.
"Even though the government has been tolerant of anti-government positions and criticisms on the Internet, we are very concerned about statements that insult religion and reek of racism," he added.
The warning comes amid increasingly frank discussions on the internet of such hot-topic issues as Malaysia's status as an Islamic state, allegedly unjust policies and political corruption.
Crackdown
Malaysian blogs and online political debates have garnered a steady following in recent years, mainly for their open discourses on politically-sensitive topics.
Until now websites have not been subject to the same government legal and administrative controls faced by the mainstream media.
But in recent months several senior government officials have called for tougher action, including new legislation to rein in those who they say belittle Islam or are seen as sowing the seeds of discord.
Late last week, a webmaster with an opposition party was detained for investigations over an alleged breach of the Official Secrets Act.
Nathaniel Tan, who works for Keadilan, the opposition party led by former deputy prime minister Anwar Ibrahim, was released after four days without any charge.
To many in the Malaysian blogosphere, the two events signal an imminent crackdown on websites and blogs critical of the government.
But not all in government are in favour of silencing critical discourse.
On Tuesday a senior leader of Gerakan, a partner in the Barisan Nasional ruling coalition, urged the government to stop trying to muzzle dissent.
Toh Kin Woon said the government should stop going after bloggers and could not promote national development by ignoring human rights.
He was quoted in the New Straits Times as saying: "Civil and political rights such as the right to free speech, dissent and assembly are as important as economic rights such as the right to a job, housing, medical care and education."