The actor's wax figure will not travel to cities including Hong Kong and Bangkok as part of the museum's plan to showcase Indian cinema in the region.
"This will be a big disappointment for Salman's fans across nations," said PR guru Dale Bhagwagar.
Wax models of Shah Rukh Khan, Aishwarya Rai Bachchan, Hrithik Roshan and Kareena Kapoor will feature in the exhibition.
"It's just been a little over four years when Salman's wax statue was inaugurated with much fanfare at Madame Tussauds," said Bhagwagar.
"Moreover, it's been a favourite among fans and also known to be one of the most photographed there, at par with the ones of Shah Rukh, Hrithik and Mr Bachchan. Strange, that it'll be missing the world tour."
The museum has chosen to use an existing waxwork figure of Amitabh Bachchan that is on permanent display in Hong Kong, rather than ship over his London statue.
The model of Kareena Kapoor was unveiled at Madame Tussauds in Blackpool rather than its central London exhibition.
A figure of Madhuri Dixit - Bollywood's most recent star to be immortalised in wax - will remain on display in the UK.