The government is trying to get a new abbot appointed to head Wat Dhammakaya, whose former leader is wanted for money laundering, an official said on Thursday.
Police pulled back from a three-week siege of Wat Dhammakaya this month after failing to find Phra Dhammajayo in a search that was frustrated by monks and devotees in one of the biggest challenges to the junta since a 2014 coup.
Phra Dhammajayo, 72, is wanted for questioning for suspected money-laundering and on numerous charges of building on land without authorisation.
The National Office of Buddhism had proposed to religious authorities that a monk with no affiliation to the temple should now be appointed to lead it, the head of the government office, Pongporn Pramsaneh, told Reuters.
This would help with an investigation into the temple's assets and in the process of disrobing Phra Dhammajayo, he said.
"The new abbot should be someone the society can rely on for unbiased action and judgment," Mr Pongporn said.
The proposal on changing the leadership was made to the most senior monk in the Pathum Thani province, where the temple is located.
The temple would respect any decision of the Sangha religious council, said senior Dhammakaya monk Phra Pasura Dantamano.
"Nonetheless, there is also a process of doing so and it is not possible to appoint someone from the outside without consulting the current temple administration," he said.
The temple's current acting abbot is Phra Dhammachayo's deputy, Phra Dattajivo, but police last week said they were investigating him for using temple money in stock dealing.
The temple said the accusation was "fake news" and that none of its money had gone into stocks.
The Dhammaka temple, nearly 10 times the size of the Vatican City, dwarfs other temples in wealth as well as size. It claims millions of followers, although still a small minority of Thai Buddhists.
Traditionalist Buddhists accuse the temple of commercialism, though it says it is just as dedicated to Theravada Buddhism as them and its money is only to do good works.
Mr Pongporn said the Buddhist governing body in Pathum Thani province would convene to inspect the Dhammakaya temple's financial records at the end of the month.
Gen Prayut Chan-o-cha, as the junta chief, used his unchallenged power under Section 44 of the interim charter to put Mr Pongporn in charge of the National Office of Buddhism in late February, when the confrontation between authorities and the temple was at its peak. Mr Pongporn was formerly a high-ranking official at the Department of Investigation, which led the siege of the monastery.