FIFA, which last week said it would take greater control over friendlies, ordered the investigation into the Latvia-Bolivia and Estonia-Bulgaria matches played in the resort of Antalya on February 9.
Latvia won 2-1 and the other game ended 2-2, all the goals coming from penalties. A FIFA spokesman said the officials would not be named.
"The proceedings were opened following an evaluation of all documentation and information received by FIFA, in relation to a possible match-fixing situation in these matches," FIFA said in a statement on Thursday.
"The FIFA Disciplinary Committee will be in charge of dealing with the matter."
Match-fixing by illegal betting rings has become a major concern for sporting authorities.
UEFA president Michel Platini has described it as the biggest scourge facing football and International Olympic Committee (IOC) president Jacques Rogge said last week it was putting sport in danger.
The four teams involved complained at the time about the refereeing.
"We had some doubts about the refereeing in this match," Bulgarian Football Union (BFU) president Borislav Mihaylov told reporters after his team's match.
Gustavo Quinteros, making his debut as Bolivia coach, told La Razon newspaper after the game: "For me, he (the referee) invented all three of the penalties, the two against us and the one in favour. It was a disgrace."
There was also confusion over the identities of the referees.
Official reports from the BFU and the Estonian FA say the referee at their match was Hungarian Krisztian Selmeczi.
However, Hungarian referees' chief Laszlo Wagner and Hungarian media have indicated the referee was Selmeczi's compatriot Kolos Lengyel.
Wagner said last month the three Hungarian match officials involved would be suspended.
"I'm shocked because we didn't receive a letter to allow these referees (Selmeczi, Lengyel and Janos Csak) to officiate at this game," Wagner told Bulgarian radio at the time.
"I can say that these three will not officiate any more matches while I'm head of the commission."
The Bolivian Football Federation asked FIFA for an identity check after their game against Latvia.
"We asked to check if the referees from the Czech Republic were the ones who took charge of the match and if they had FIFA credentials," it said a statement published on its website.
FIFA said last week it would tighten the rules over friendlies, which until now have been a free-for-all with no control from football's governing body.
FIFA said it would have to be informed who was refereeing each match and that it would intervene in the future if it saw anything suspicious.
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