I am writing this column from an airplane, on my way from Kuala Lumpur, Malaysia, to my new home, Wellesley, Mass. I’m in a comfortable seat, and I’m looking forward to getting back to my family. About 12 hours ago, though, I was miserable, locked in a holding cell by Malaysia’s “religious police.”

The story began a few months ago, when the Islamic Renaissance Front, a reformist, progressive Muslim organization in Malaysia, invited me to give a series of lectures on Islam, reason and freedom. The group had hosted me three times before in the past five years for similar events and also published the Malay version of my book “Islam Without Extremes: A Muslim Case for Liberty.” I was glad for the chance to visit Malaysia again.

I arrived in Kuala Lumpur on Sept. 22. The next day I gave my first lectureon the suppression of rational theology by dogmatists in early Islam, making the point that this “intellectual suicide” still haunts Muslim civilization.

The second talk was on a more controversial topic: apostasy from Islam. I argued that Muslims must uphold freedom of conscience, in line with the Quranic dictum “No compulsion in religion.” I said that apostasy should not be punished by death, as it is in Saudi Arabia, or with “rehabilitation,” as it is in Malaysia. The practice of Islam must be on the basis of freedom, not coercion, and governments shouldn’t police religion or morality.

It turns out all you have to do is speak of the police and they will appear.

At the end of my talk, a group of serious-looking men came into the lecture hall and showed me badges indicating that they were “religion enforcement officers.”

“We heard that you just gave an unauthorized talk on religion,” one of the men said. “And we got complaints about it.” They took me to another room, photographed me and asked questions about my speech.

When they were done with their questioning, they handed me a piece of paper with Malay writing on it and told me that I shouldn’t speak again without proper authorization. They also warned me away from my next planned talk, which was going to be about my most recent book, “The Islamic Jesus: How the King of the Jews Became a Prophet of the Muslims.”

“We heard that you will speak about commonalities between Islam, Judaism and Christianity,” one officer said. “We don’t like that kind of stuff.” Then they left.

After all this, I consulted with my hosts, and we decided to cancel the final lecture. I assumed that was the end of the matter and went shopping for gifts for my wife and children.

Later in the day, I went to the Kuala Lumpur International Airport to begin the 30-hour trip back to Massachusetts. When I gave my passport to the border police, I realized that my experience with offending Malaysia’s Islamic sensibilities wasn’t over.

“You need to wait, sir,” said the woman who checked my passport. She called some police officers, who called other police officers, who took me to a room where my arrest order was read to me. Apparently the religious police, known as JAWI, wanted to interrogate me again for my “unauthorized” talk on religious freedom and had issued that arrest order to make sure I didn’t leave the country.

I was taken from the airport to a police station, then to another station. Finally, I was taken to the JAWI headquarters, where I was locked up.

To be fair, nobody was rude to me, let alone cruel. Still, I was distressed: I had been arrested in an alien country whose laws and language I did not understand. I had no idea what would happen to me — and, most painfully, when I would see my wife, Riada, our 2-year-old son, Levent, and our 2-month-old baby, Efe.

In the morning, I was taken to a Shariah court, which is used in Malaysia to adjudicate religious issues, where I was interrogated for two hours. At the end, to my surprise, I was let go. Soon I learned that this was greatly facilitated by the diplomatic efforts of my country, Turkey — and especially the contact made by a former Turkish president, Abdullah Gul, with Malaysian royalty.

This incident showed me once again that there is a major problem in Islam today: a passion to impose religion, rather than merely proposing it, a mind-set that most Christians left behind at the time of the Inquisition.

Luckily, there are antidotes within Islam to this problem. One of them is the Quranic verse that the JAWI officers repeatedly chided me for daring to recite: “No compulsion in religion.”

In fact, mainstream Muslim tradition, reflecting its illiberal context, never fully appreciated the freedom implied by this verse — and other ones with similar messages. “The ‘no compulsion’ verse was a problem to the earliest exegetes,” as Patricia Crone, a scholar of Islamic history, has noted. “And they reacted by interpreting it restrictively.” The verse was declared “abrogated,” or its scope was radically limited.

This is still evident in a parenthetical that is too frequently inserted into translations of the verse. “There shall be no compulsion in religion (in becoming a Muslim).” I’d known that Saudi translations added those extra words at the end. Now I have learned that the Malaysian authorities do, too. They append the extra phrase because while they agree with the Quran that no one should be forced to become a Muslim, they think that Muslims should be compelled to practice the religion — in the way that the authorities define. They also believe that if Muslims decide to abandon their religion, they must be punished for “apostasy.”

One of the officers at my Malaysian Shariah court trial proudly told me that all of this was being done to “protect religion.” But I have an important message for her (which I didn’t share at the time): By policing religion, the authorities are not really protecting it. They are only enfeebling their societies, raising hypocrites and causing many people to lose their faith in or respect for Islam.

I came to understand that while I was being held in the JAWI headquarters, listening to a loud Quranic recitation coming from the next room. I heard the Quran and for the first time in my life it sounded like the voice of an oppressor. But I did not give in to that impression. “I hear you and I trust in you, God,” I said as I prayed, “despite these bigots who act in your name.”