Spurs manager Villas-Boas expected Bale to report to the club's training ground in Enfield on Tuesday, but unlike the rest of his team-mates, the 24-year-old did not show.
The Welshman has always reported to the Hertfordshire base for treatment on his supposed foot injury ever since it stopped him from playing for the north London club last month.
But the forward did not turn up on Tuesday and no explanation has been given as to why.
A Spurs source said there was ''no issue'' with Bale not turning up, and insisted that the player remained in touch with Villas-Boas about his training regime.
This contradicted earlier reports that Bale was ''furious and frustrated'' with Tottenham's handling of his proposed world-record transfer to Madrid.
Villas-Boas is expected to set the record straight on Wednesday, however, when he gives a press conference at 12:30pm to preview the team's Europa League playoff game against Dinamo Tbilisi.
Press Association Sport understands that Bale's absence does not mean he is closer to a move to Madrid, despite reports in the Spanish media that the former Southampton winger could seal his move to Real in the coming days.
Tottenham insist they will not sell Bale to Madrid until they have signed at least one more player to replace him.
Talks in London are ongoing with Roma over the possible transfer of midfielder Erik Lamela, but Villas-Boas' hopes of being reunited with Zenit St Petersburg forward Hulk look set to be dashed after the club's manager Luciano Spalletti said the Brazilian was not for sale.
Real's hand has been weakened over the course of the last week thanks to their decision to erect a stage that was reportedly set to be used to unveil Bale on Tuesday.
It is understood that Spurs chairman Daniel Levy has also not taken kindly to the idea that Real started selling replica shirts with Bale's name on the back, and their offer to spread the world-record fee for Bale over six years.
Bale spent the weekend in Marbella after Villas-Boas gave him the weekend off, but he was back in London on Tuesday for a meeting with his agent Jonathan Barnett.
The forward is now expected to miss the club's Europa League clash against Dinamo Tbilisi on Thursday night.
Former Spurs midfielder Glenn Hoddle has claimed Levy still harbours hopes of holding on to Bale, who scored 31 goals for club and country last season.
''I was at the Swansea game at the weekend and had a good chat with Daniel Levy,'' Hoddle told talkSPORT.
''He's ambitious and believes, if Bale was to stay, that Tottenham could go on and do something really strong in the Premier League.''