However, Thomas has released photos on social media of herself with 25-year-old partner Alex Roberts.
She changed her Facebook profile picture to a snap of the two enjoying sushi and cocktails on a romantic holiday.
The pair, who have been dating for five months, were subject to jokey comments from friends who, referring to the Cruise rumours, said that Mr Roberts "looks different in the movies".
Miss Thomas, an investment banker's daughter from Hertfordshire, became Cruise's assistant while working on the new Mission Impossible film.
She met Mr Roberts, the director of a carpentry firm from Ashford, Middlesex, on the set.
They have since enjoyed holidays in Italy, Miami, Abu Dhabi and Atlanta.
A source told The Sun: "It's still early days between Emily and Alex but they're already pretty close. They've been very public with their relationship, so reports concerning Tom [Cruise] will come as a surprise to pals."
- Daily Mail