The Foreign Ministry cancelled the missing visas and launched an investigation in July. The embassy has sought legal action against five of its local staff.
Immigration authorities of both countries were alerted.
Nine foreigners have been arrested trying to enter Thailand with the stolen stickers.
“A check into the history of the nine foreigners detained for using the missing visas found they are in a risk group of terrorism and transnational criminals,” Pol Lt General Panu Kerdlarbpon, Immigration Police Bureau commissioner, said without elaborating.
The nine were two Iranians, three Nigerians, two Indians and two Pakistanis. Two of the Nigerians were arrested yesterday by immigration officials in the border province of Songkhla.
The investigation showed that 259 of the 300 stickers had been used and 55 visa holders were still in Thailand.
Panu declined to reveal whether the theft gang had Thai accomplices.
Earlier Jakkrit Srivali, deputy Foreign Ministry spokesman, said the embassy in Kuala Lumpur had alerted immigration authorities in both countries after hundreds of visa seals went missing, saying they could be used for illegal purposes.
The ministry had known about the theft for some time but kept it out of the media to facilitate the investigation and neither side wanted those who used the stolen stickers to escape across the border, he said.
An investigation team of officials from the embassy and the ministry in Bangkok has been pursuing the case since last month and found that the gang had covered their crime very well.
“Our investigation shows that some Thais in Thailand were involved but there was no participation by any ministry officials. We will be taking legal action against the perpetrators,” he said.