Justice Minister Pracha Promnok told reporters that the speculation had been dreamt up by a “frantic” media.
The king is due to grant an amnesty to thousands of convicts to celebrate his birthday on 5 December.
Mr Thaksin was convicted on a fraud charge, but lives in exile to avoid serving a jail sentence.
The current amnesty plan covers only serving prisoners, and excludes people found guilty of fraud.
But local media claimed the government, led by Mr Thaksin’s sister Yingluck, was trying to change the rules of the amnesty to include the former prime minister.
The Bangkok Post newspaper fuelled the speculation last week when it quoted a government insider as saying a secret cabinet meeting had been held to discuss the issue.
A group of anti-Thaksin protesters announced they would hold rallies to denounce the move, threatening the kind of chaos that has crippled Thailand in recent years.
But Mr Pracha insisted the original amnesty rules would not be tampered with, saying: “Convicts on the run will not be eligible.”
His statement appears to have calmed tensions, with protesters calling off their planned rally.