Prime Minister Prayut Chan-o-cha has insisted the report on a "network of elements sabotaging the nation" was intended for his eyes only and not for anyone else to see.
The report was spotted on Gen Prayut's table in the parliament chamber during a debate on Wednesday on the prime minister's oath recital gaffe.
A picture was taken of the report -- titled Khrongkhai Khabuankan Tamlai Prathet, which means "network of elements sabotaging the nation" -- on the premier's desk, which immediately led to speculation about the report's contents.
A government source said the document was a report prepared for a briefing by intelligence and security agencies. The "elements" are believed to be political figures, whose actions are deemed to have offended the high institution of the monarchy.
Gen Prayut said on Thursday the report was not meant to be seen.
Government spokeswoman Narumon Pinyosinwat said it was classified information compiled by the security agencies.
She denied the premier deliberately put the report on the table so the media would see it. The snapshot of the report has led to some thinking the government was issuing a veiled warning to its critics.
Ms Narumon said Gen Prayut handles a lot of paperwork each day and it was possible the report was mixed among the documents he brought into the chamber.
Pheu Thai Party chief strategist, Khunying Sudarat Keyuraphan, said Gen Prayut should not see his critics as those wishing to sabotage the country.
Deputy Prime Minister Prawit Wongsuwon, meanwhile, said no details of the report could be divulged, although he insisted it had nothing to do with politics.