More investigations and arrests are expected to follow, with 30 temples suspected of involvement in financial crimes running into millions of dollars.
The raids, carried out by more than 100 police officers, follow a similar mission last year to arrest the abbot of Dhammakaya temple, Thailand's biggest and wealthiest Buddhist sect, excoriated for promising followers good karma and a noble afterlife in return for big cash donations.
Police laid siege to the vast domed Dhammakaya temple on the outskirts of Bangkok in what became a cat-and-mouse game that dragged on for several weeks to arrest Phra Dhammajayo on embezzlement charges.
The former abbot, subsequently stripped of his monastic rank, managed to evade capture and flee the country. The Government quietly retreated as criticism mounted over its heavy-handed tactics.
It may have lost out on a big catch, but the Government dealt a blow to the sect's credibility and broke the historic taboo of state action against monks.
In Thailand, there are about 40,000 temples, which generate billions of dollars a year in donations.
But scholars say true piety among monks and lay people has waned and been replaced by an emphasis on donations and gestures that yield instant karma.
At Wat Saket, one of the temples in Bangkok raided by police, tourists blithely ring enormous bells, chatter, and chomp on ice cream at the temple's peak. Spirituality is palpably lacking.
Duncan McCargo, a Thailand expert and professor of political science at the University of Leeds, said corruption in the monastic community is endemic, with the temples that were raided having drawn negative attention.
"The particular temples and monks that are the focus of these raids are controversial and have been on the outs for some time. This is especially true with Wat Saket, a top-ranking temple that no member of the royal family has visited for decades because it has long been seen as untrustworthy," he said.
Stories of monks engaging in unseemly pursuits have spawned considerable cynicism among younger Thais.
"I don't go to temples much these days. I don't feel I believe in them," said Pannaporn Ketsawat, 27, a call-centre worker.
Thai identity has long been self-defined by the institutions of "Nation, Religion, Monarchy." But Buddhism here has been in a state of crisis for many years.
Latent sectarian divisions have for decades created something of a power struggle between the dominant Thammayut and Maha Nikaya sects, the former enjoying a reign that parallelled that of the late King Bhumibol Adulyadej, who died in 2016.
Hailing from the Maha Nikaya order, Dhammakaya has grown rapidly, with hundreds of thousands of followers, and poses a political and constitutional threat, not least because it has been closely associated with former Prime Minister Thaksin Shinawatra, a populist who was accused of corruption, branded as an authoritarian and deeply opposed by the military and elites.
The country's lack of secularism means the line between religion and politics is often blurred.
"Although it may appear that the secular government is imposing its own views on religion, it is certain that there are also religious considerations behind the scenes," said Gregory Seton, a professor in the religion department at Dartmouth College
Since coming to power in a bloodless coup in 2014 on the back of a pledge to sweep out corruption, the military has sought to exercise more control over Buddhism.
The Government has moved to inspect the finances of all temples and requires monks to keep smartcards that identify their political and religious backgrounds, said Paul Chambers, an expert on Thai politics at Naresuan University in northern Thailand.
"The raids are motivated by a junta desire to control Buddhist monks of all persuasions," he said.
Officials from the government and relevant state agencies did not respond to or could not be reached by requests for comment.
The arrest of Phra Buddha Issara targeted a monk who would seem to have been on the same wavelength as the junta. He helped lead the anti-government marches that paved the way for the toppling of the Government of Yingluck Shinawatra, Thaksin's sister, and has been a staunch advocate of cleaning up Buddhism.
He served in the 21st Infantry Regiment, Queen's Guard, which Prayuth formerly commanded. There was no career overlap, said Mano Laohavanich, a former monk and outspoken critic of Wat Phra Dhammakaya, but they are known to be close. Prayuth has publicly denied this.
Buddha Issara has been charged with the serious crime of forging the late king's royal insignia to stamp amulets and supporting robbery during demonstrations against Thaksin's sister.
The forgeries allegedly happened in 2011 but were brought to the attention of police in 2017 by the Buddhism Protection and Promotion Organisation, whose members claim to be defenders of the religion.
Suraphot Thaweesak, a Buddhism scholar, said the fact that the accusation and charge in the alleged forgeries have only recently come to light suggests the "situation wasn't ripe" to expose it earlier.
"There's nothing certain in Thailand. It depends on when the power holder thinks it's time to execute," he said.
