Spain, Portugal and Qatar are being investigated in connection with alleged collusion over voting for the 2018 and 2022 World Cups, BBC Sport understands.
Spain and Portugal are making a joint 2018 bid, while Qatar is eyeing 2022.
The probe is part of a wider inquiry by world governing body Fifa into alleged breaches of the bidding rules.
On Thursday, the chief of the Portuguese Football Federation Gilberto Madail rejected allegations of any collusion with other candidates.
"We received with surprise and indignation the analysis that Fifa's ethics committee may conduct on a rumour circulated in September in the English media about an alleged deal between the Iberian and the Qatari bids for hosting the World Cup," said Madail.
"It is odd that there is an attempt to launch completely unfounded suspicions about the Iberian bid at a time when there are news reports about alleged vote-selling for the 2018 and 2022 World Cups involving other bids."
Fifa's ethics committee is to report in November after launching separate inquiries into six Fifa officials and two of the bidding candidates.
Collusion between bidding countries is explicitly forbidden by the regulations, but Fifa chiefs have ruled out postponing the 2 December vote for the 2018 and 2022 World Cup hosts.
England are bidding for the 2018 finals and are competing against Russia as well as joint bids from Spain and Portugal and Holland and Belgium.
Qatar, Australia, the United States, Japan and South Korea are contesting the 2022 vote.
Fifa's investigation will run alongside the ethics committee's probe into two senior Fifa officials who have been provisionally suspended after being caught up in a World Cup cash-for-votes scandal.
Amos Adamu from Nigeria and Tahiti's Reynald Temarii, both members of Fifa's 24-man executive committee which will decide on the 2018 and 2022 World Cups, were trapped by a Sunday Times undercover investigation in which they appeared to offer their votes in return for payment.
Adamu, 57, allegedly said he wanted $800,000 (£500,000) to build four artificial football pitches. This would be against Fifa's rules.
Adamu has since denied any wrongdoing, saying: "I wholly refute all allegations made."
Tahitian Temarii, 43, who played for French club Nantes during the 1980s, is alleged to have asked for a payment to finance a sports academy. He has already pleaded his innocence.
The pair appeared before the ethics committee yesterday and were suspended "from all football activity" pending a final hearing next month.
Four other Fifa officials - Slim Aloulou, Amadou Diakite, Ahongalu Fusimalohi and Ismael Bhamjee - have also been provisionally suspended from taking part in any football-related activity.