Webber has been with Red Bull since 2007, when they were a midfield contender.
But the team have made it clear that they are building their future around 23-year-old Vettel, who joined in 2009 after being part of their driver development programme.
The issue of the team's apparent preference for Vettel has been a running theme this season .
Webber led the championship for the first time this year after the Monaco Grand Prix in May. He lost it to Hamilton, regained it, and then lost it to Alonso after crashing out of the last race in South Korea two weeks ago, where Vettel retired from the lead with an engine failure.
When Webber's comments were put to team principal Christian Horner, he said: "It's not inconvenient (that Mark has been leading the championship).
"Mark has had tremendous support from the team. The team have given him a great car and we've done our best to give them both equal equipment.
"I'd have to understand what Mark was meaning by those comments. He's probably referring to the support of Sebastian by Helmut Marko (Red Bull's special adviser, who is close to team owner Dietrich Mateschitz).
"But that doesn't change how the team operate. Dietrich has always been very clear - he doesn't mind whether it's the oldest or the youngest world champion. We've given both as much support as we can.
"Obviously it would have been very convenient for Mark if we'd said Seb would be his rear gunner for the last few races. But that was never going to be the way we went racing - whichever way round the drivers were."
The controversy was heightened in the last week when former F1 driver Gerhard Berger, who is close to Mateschitz, said on Red Bull's own TV station that he thought Webber had let his car run back across the track after his crash in Korea in an attempt to take out one of his championship rivals - he ended up hitting Mercedes's Nico Rosberg.
Webber responded sarcastically to those remarks on Thursday by saying: "First of all, I lost control of the car and then I've regained control and tried to take someone out. I'm a bit of a genius, aren't I?"
He added: "Gerhard has had some pretty nasty accidents in his time and so have I. I would never put myself or anyone else in any more danger than I need to."
Horner said Berger's comments were "purely his personal view".
He added: "They're nothing to do with the team and it's certainly not a team view. We have always believed in freedom of speech."
Horner admitted that the team were open to the possibility of asking one driver to support the other in one of the final two races if the mathematics of the championship made it the obvious tactic.
Vettel said he was still "full of hope" that he could win the world championship.
"We've seen how much things can change in one weekend," he said.
With Alonso's team-mate Felipe Massa making it clear he will help Alonso, McLaren are also in the awkward position of deciding when to ask Button to do the same.
Team principal Martin Whitmarsh said this week that the team would make the decision depending on the situation in the race.
Button said that this weekend they would not be allowed to do that as team orders are banned in F1, but that he would make his own decision on the matter.
"[Martin] won't ask me, no," added Button. "The team won't ask me to do anything because that's illegal.
"If I can't win the race, I'll make what I feel is the right decision during the race and it will be entirely my decision."
Hamilton agreed that he did not need Button's help on the track and that the best outcome would be for McLaren to perform strongly as a team.
"We can help ourselves by just getting the best out of the car," added Hamilton.
"It would be great to have both of us at the best that we've been all year, both of us right up there and doing that to divide the group - that's the only way we can help each other."
Hamilton needs results to go his way on Sunday if he is to regain the title he won at Interlagos in 2008, but he remained upbeat about his chances.
"It is still in my hands and I am generally quite relaxed," said Hamilton.
"Whatever results I'm able to achieve puts me in a stronger or weaker position. I just have to finish ahead of them and hope what goes on behind me is positive for me.
"If I win the next two races I put myself in the best position possible. I never have problems giving up. I always push to the last moment.
"The gap seems a lot but anything can happen."
Button, who captured his 2009 crown in Brazil, conceded it has now become difficult to defend his title.
"I want to fight for it again," Button said. "Most of this season I have been fighting for the world championship. Now it's very difficult to continue fighting, but there's still a bit of hope.
"I want to win the race so that's my main aim. It'll be pretty close around this circuit which makes the fight for the title even better."
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