Information Department deputy chief Jakkrit Sriwali Thursday described the missing labels as an ‘‘irregularity’’ caused by Malaysian staff employed at the embassy.
Mr Jakkrit said tough legal action would be taken against those responsible, including Thai nationals.
The 300 visa slips were found missing from the embassy after border police officers arrested a Nigerian national who was on the immigration watch list.
The arrest of Sunday Edwin Naemeka, 35, which exposed the scandal, took place at Songkhla Immigration Office in Sadao district on the Thai-Malaysian border on Wednesday morning.
Mr Jakkrit said officials had known about the disappearance of the slips for some time, but the case had not been made public because the Foreign Ministry did not want those holding the illegally obtained visas to know they were being hunted.
Two committees have been set up to investigate the incident, one by the Thai embassy in Kuala Lumpur and the other by the Foreign Ministry.
The ministry’s committee went to Kuala Lumpur last month to conduct its probe, Mr Jakkrit said, adding that they found that those responsible for the crime had tried to cover their tracks.
The Thai suspects involved are believed to be outsiders without links to immigration authorities, he added.
There are five Malaysian employees in the consular section of the embassy.
Deputy Prime Minister Pracha Promnok Thursday confirmed the loss of the visa labels. He said a Cameroonian and a Guinean were caught using two lost visa labels trying to enter Thailand from Laos through Mukdahan province on July 20 and 21 respectively.
Thai authorities knew something was amiss because the foreigners had not entered Malaysia but their stamps were marked by the Thai embassy in Kuala Lumpur.
A number of other foreigners were arrested at Suvarnabhumi airport trying to use the lost visa labels. They were charged with using fake documents to enter the country and detained at the Immigration Bureau in Bangkok.
Pol Gen Pracha said the authorities do not know if the visa scam is linked to terrorism.
The Foreign Ministry has nullified the lost visa labels, he said, and added that he hopes the ministry will find the culprits. It will be important to find out why the scam took place at the Thai embassy in Kuala Lumpur, he said.
Immigration Bureau commissioner Pol Lt Gen Pharnu Kerdlarpphon said 103 foreigners used the visas to enter the country, and 59 of them have since left Thailand.
Immigration police in Songkhla’s Sadao district Thursday apprehended Kimba Yaou, a 35-year-old citizen of Niger, with a lost visa slip.
The Nigerois said he was a football player and he had paid US$1,000 (about 30,000 baht) to a broker in Kuala Lumpur to get a visa for him. He wanted to enter Thailand to visit his pregnant Thai wife.
The 44 remaining in the country include 26 Nigerians, six Indians and the rest from Central Asia.
According to the commissioner, 11 foreigners have been arrested with the lost visa labels. They comprise three Pakistanis, three Indians, two Iranians, a Cameroonian, a Guinean and a Russian.
Some of them said they had received visas in front of the Thai embassy in Kuala Lumpur and others said they got visas in Thailand.
Immigration police are looking for a Thai woman identified only as Mama as she is suspecting of selling a lost visa label to the Cameroonian. Detectives said the woman was a major visa broker in Thailand.
Army commander Prayuth Chan-ocha said that the loss of the visa labels should not pose any security problems in Thailand.