After weeks of bargaining, Thailand's offer had reportedly been approved by the Premiership club's board and Thai negotiators said the two sides were undertaking "due diligence" checks of the club's financial integrity.
But today Shinawatra cast doubts on whether the deal would materialise.
"At this moment, I am not certain that we can buy it or not," he said, refusing to elaborate.
"Our financial experts and the legal team are performing the (due diligence). But nothing is certain. If it is affordable to buy we will buy, if not we will not."
Shinawatra had originally indicated that he would buy the Liverpool stake with his own money.
But the government later said it would be owned by a new company to be set up under the government's Sports Authority of Thailand.
Liverpool are due to announce their new manager in the next fortnight after sacking Gerard Houllier. Valencia's former coach Rafael Benitez is the favourite for the job.