Boro had agreed an initial £7m fee, rising to £20m with add-ons, for the 21-year-old, and the defender had already travelled to Rockliffe Park last week to complete the switch before the issues emerged.
Talks between the two clubs remain ongoing, with Middlesbrough now exploring the possibility of restructuring the deal as an initial loan rather than a straight permanent transfer.
Phillips came through the academy at Blackburn Rovers, making 14 appearances there before Tottenham triggered his £2m release clause in 2023 when he was 18. Despite entering his fourth season as a Spurs player, he has yet to make a first-team appearance for the club, spending time on loan at Plymouth before two seasons at Stoke City.
Should Middlesbrough complete the move, it would extend a busy summer for Kim Hellberg's side, who have already brought in Jeremy Sarmiento, Will Lankshear, Radek Vitek, Sebastian Berhalter and Kyle Joseph, funded in part by a significant sell-on fee from Morgan Rogers' £116m move to Chelsea from Aston Villa.
Boro opened their season with a 1-0 win over Wrexham in the first round of the Carabao Cup on Friday.
Tottenham's other significant transfer story centres on midfielder Lucas Bergvall, who continues to attract interest from Newcastle United despite the north London club rejecting an earlier bid from the Magpies.
According to Fabrizio Romano, Newcastle have not cooled their pursuit of the Sweden international, even after a change of manager at St James' Park, with Eddie Howe's exit paving the way for Matthias Jaissle.
Newcastle United are understood to have had a verbal offer in the region of £45m rejected, with Tottenham said to be holding out for a fee closer to £50m-£60m given the arrivals of Sandro Tonali and Mateus Fernandes in Spurs' own midfield have made Bergvall's path to regular football less clear.
Nottingham Forest had also been credited with interest in the 20-year-old, though their focus is understood to have shifted towards AC Milan's Tijjani Reijnders instead, potentially clearing the way for Newcastle to press ahead with a fresh approach.