Officers began raiding the site on Thursday after previous attempts were thwarted when thousands of the monk’s devotees turned up in his defence.
The Wat Dhammakaya temple was earlier placed under military control.
The spiritual leader is believed to be hiding inside the large compound.
Phra Dhammajayo is accused of embezzling funds from the huge temple in Bangkok, but when officers attempted to search the site last June they were blocked by his supporters.
The 72-year-old abbot has remained inside the temple for months, saying he is too ill to face officials. He denies the allegations and says they are politically motivated.
Earlier on Thursday hundreds of police and soldiers surrounded the site, blocking the roads leading to and from the temple and putting the area under military control.
“We are sealing off the temple and after that we will search all the buildings,” said Col Paisit Wongmaung, head of the Department of Special Investigations (DSI).
“If [the abbot] thinks he is innocent he should surrender and enter judicial process,” he said.
Some 4,000 police and military were deployed with blockades “prohibiting anyone from entering or leaving”, the temple said in a statement.
There have been several failed attempts to persuade the former abbot to leave the temple.