PATHUM THANI, Thailand—Phra Dhammachayo, a Buddhist monk, shouldn’t be too hard to find.

With his orange robes and dark glasses, the 73-year-old is one of Thailand’s best known figures. His temple, just north of Bangkok, is ten times as large as Vatican City and hosts a vast, flying-saucer shaped dome where many of his three million followers meditate.

But the monk has been missing since March after officials issued a warrant for his arrest, accusing him of knowingly accepting millions of dollars stolen from a local credit union and other charges. Police say they have no idea where he is. Phra Dhammachayo’s representatives say he hasn’t done anything wrong.

Thailand’s junta is eager to find him for reasons other than the fraud charges, say people familiar with the generals’ thinking. Their specific concerns, these people say, are that his temple has grown so quickly, and that Phra Dhammachayo has close ties to ex-Prime Minister Thaksin Shinawatra, who was ousted in a 2006 coup and is still popular among Thailand’s poor.

Mr. Thaksin’s government dropped an earlier probe into alleged fraud of the temple’s finances. His sister Yingluck Shinawatra, a subsequent Thai prime minister, tapped the Dhammakaya Temple to help form a Buddhism school curriculum before she, too, was ousted in a putsch.

The generals also are alarmed by some of the temple’s more esoteric teachings, which borrow heavily from Chinese mysticism and encourage the use of meditation to drive out what Phra Dhammachayo has called the “forces of darkness” from Thailand.

“They think it’s almost a state within a state,” one of these people said.

Thai Buddhist abbot monk Phra Dhammajayo, center, surrounded by Buddhist monks as he arrives to preside over a ceremony to mark the Makha Bucha Day at Dhammakaya Temple, March 4, 2015 PHOTO: RUNGROJ YONGRIT/EUROPEAN PRESSPHOTO AGENCY

Pasura Dantanamo, a senior monk at the temple, said it isn’t allied with any political group. He pointed out that some of Mr. Thaksin’s political opponents also worship at the temple. Mr. Thaksin, who lives abroad, also denies plotting against the government.

A lot has changed in Thailand since the latest coup brought the generals back to power three years ago. They have jailed or exiled dissidents. The once-roaring economy has stumbled as foreign investment slowed. A new king, King Maha Vajiralongkorn, recently succeeded his father King Bhumibol Adulyadej after more than seven decades on the throne.

But Phra Dhammachayo’s fall from grace is among the more striking story lines to emerge.

For 23 days this spring, some 4,000 riot police and soldiers besieged the Dhammakaya Temple, butting up against monks and protesters trying to defend their guru. In March, investigators took the hunt nationwide after finding a hole chiseled in the temple’s perimeter wall. Some suspect the monk might have fled the country.

It’s a jarring reversal from the years when Phra Dhammachayo was courted by tycoons and politicians, notably Mr. Thaksin. Born Chaiyabun Siddhipol, he studied economics before ordaining and taking the monastic name Phra Dhammachayo (phra is a Buddhist honorific, like reverend).

His Dhammakaya Temple preaches a new, modern take on Buddhism seasoned with the kind of prosperity gospel taught by some Pentecostal groups, and was tailor-made for the middle classes who emerged during Thailand’s boom years in the 1980s and 90s.

Parts of the complex resemble a state-of-the-art airport, all brushed concrete and steel. The dome is made out of 300,000 palm-sized Buddha statues which can be sponsored for 10,000 baht, or around $300 apiece.

“Dhammachayo was a wonderful seller of new ideas, but he is also an opportunist who was in the right place at the right time,” said Mano Laohavanich, a physician and former monk who said he left the temple in 1995 over his concerns about its growing wealth.

Thai Buddhist monks from Dhammakaya Temple confront soldiers outside the temple, February 23, 2017. PHOTO: EUROPEAN PRESSPHOTO AGENCY

Now, Phra Dhammachayo is now in the junta’s sights. Prosecutors want him arrested for allegedly laundering money embezzled from a credit union, and have a list of over 350 charges relating the temple’s finances.

“It doesn’t matter if he’s famous or not,” said Police Colonel Worranan Srilum. “What matters is that he is a wanted man. It’s our duty to find him and bring him in.”

Phra Dhammachayo’s aides said he was too ill to acknowledge the charges. On one occasion he said he was too busy planning his birthday party, investigators said.

The monk won’t be taken easily.

On the few times that investigators managed to get inside the temple, they failed to find any sign of Phra Dhammachayo. One group of police thought they had found a long tunnel leading out of the temple complex and took a team of television reporters to investigate. It turned out to be a dead end, leading to a water riser.

Other officers said they thought they spotted Phra Dhammachayo hiding in his living quarters, but it turned out be just a jumble of pillows.

Said one former army officer, Lt. Gen. Nanthadej Meksawat, “I’m starting to believe that Dhammachayo has mysterious powers. How else could he have escaped the siege?”