Prayuth, then the army chief, overthrew the Government of Thaksin's sister Yingluck in a 2014 coup. His junta discovered dozens of weapon caches belonging to groups they said were loyal to the Shinawatra clan.
The junta said the stockpiles showed there were groups trying to create instability and justified their seizure of power.
Police chief Jakthip presented no other evidence of an assassination plot, but said Wuthipong and his network had always opposed the junta and the group had predicted on social media that the prime minister would be killed.
Police said the group was planning an ambush if officials had continued their operations against a influential nearby Buddhist temple, which is seen as having close ties to Thaksin.
Thai police ended their search of the Dhammakaya temple earlier this month after laying siege to it for more than three weeks without finding the former abbot, who is wanted for suspected money-laundering.
- Reuters, AAP