The billionaire telecoms tycoon-turned-prime minister, who was toppled by a coup in 2006, sits at the heart of Thailand's bitter political divide and now lives in self-exile to avoid jail on a corruption charge.
The foreign ministry said it was asked to take action against Thaksin after police deemed that "part of his interview endangered national security or national reputation".
It was not immediately clear which interview was being referred to or why it was deemed to breach security rules, but last week Thaksin made rare public comments in an overseas interview broadcast on CNN and at the Asian Leadership Conference in Seoul.
In its statement the foreign ministry said two passports belonging to Thaksin had been cancelled with effect from May 26.
Since going into self-imposed exile, he has travelled frequently and has been based in Dubai.
"The Foreign Ministry decided that reasons cited (by security agencies and police) were enough to cancel his passport under the ministry's regulations," the statement said.
It was not immediately possible to confirm the impact the move would have on Thaksin's ability to travel but he is also believed to hold passports from other countries.
In a CNN interview broadcast last week as Thailand marked a year since the military takeover Thaksin said he would wait for the right moment to re-enter Thai politics.