Fifa president Sepp Blatter is set to win a fourth term in office as an election delay now appears unlikely.
Prince William had backed calls for Wednesday's vote to be postponed following allegations of corruption.
But the English Football Association and its Scottish counterparts have struggled to find widespread support for their proposal.
Blatter is the only candidate for the Fifa presidency as rival Mohammed bin Hammam is suspended.
A spokesman for Prince William said: "The Duke of Cambridge, as FA President, has been kept informed of the FA's proposals and is fully supportive of the Chairman and the initiatives the FA has recommended.
"He considers the transparency of the international governing body to be integral to the good governance of the game."
Despite the support from Prince William, the FA and SFA bid to suspend the election looks unlikely to garner the number of votes - 75% of the 208 nations in Fifa - required to change the agenda.
Fifa executive committee member Chuck Blazer was disparaging about the FA's attempt to force a postponement to proceedings, insisting the move should have come much earlier.
"Unfortunately with them, everything is too little, too late," said Blazer.
"If they wanted other candidates they should have done things before the deadline.
"If they wanted to report malfeasance they shouldn't have waited for a Parliamentary hearing.
"The FA needs to learn to be ahead of the curve and not behind the game."
The FA had already decided to abstain from the voting process but chairman David Bernstein said the organisation was duty bound to make a stance.
"I think it was important that someone stood up and make a statement," he told BBC Sport. "There are some principles involved here and it's important that if nobody else was doing it then the FA took a lead in this.
"The fact that we've opposed something and taken a different view should not mean that we are isolated.
"Whatever happens, we have to be part of Fifa, there is no question of breaking away, but we would like to see better process in terms of election and governance."
The election of Fifa's president is the 14th item on the agenda at its Congress in Zurich, with proceedings expected to get under way at 0830 BST.
The build-up to the elections has been mired by a series of corruption claims but Blatter, 75, has insisted that there is no crisis.
Bin Hammam, president of the Asian Football Federation, and Fifa vice-president Jack Warner were provisionally suspended by Fifa's ethics committee over allegations that financial incentives were offered to Caribbean Football Union (CFU) members.
Blatter was also investigated following a charge against him by Bin Hammam, although Fifa's ethics committee did not find that the president had a case to answer.
Bin Hammam has appealed against his ban, while Warner, who is also president of Concacaf, the governing body for football in North America, Central America and the Caribbean, also denies any wrongdoing.
Click to play
Uncomfortable moments as Fifa president Sepp Blatter answers questions from the media on Monday
Despite the continuing claims and counterclaims, BBC sports editor David Bond said anything other than a Blatter victory on Wednesday would be hard to imagine.
"I understand that the FA and SFA are struggling to get support from the other home nations," he said. "The Welsh and the Northern Irish are not necessarily prepared to fall in behind the call to suspend the elections.
"After 13 years in charge of Fifa, Sepp Blatter has built up a huge power base inside the delegation.
"One European delegate described him as superman. The mood around the delegates that I've been speaking to is very much that even those who are opposed to him now accept there is no alternative.
"The FA has left it too late and many question whether they are just being vengeful after that England 2018 World Cup defeat last December.
"It is very difficult to escape the conclusion that Sepp Blatter will be re-elected but the question is how damaged he has been by this whole affair."
On Tuesday, Blatter addressed the opening of Fifa's congress by saying: "I thought we were living in a world of fair play and respect and discipline.
"I unfortunately see this is no longer the case because the famous Fifa pyramid is suddenly unstable and there is a danger.
"On Wednesday, I will speak to you on this danger that is lurking and tell you how we can fight and work against this threat."
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