A deal had seemed close earlier this week, with Lyon president Jean-Michel Aulas confirming that the clubs were in talks.
However, a statement on Lyon's website this evening has suggested that the move in jeopardy.
It read: "Olympique Lyonnais have not reached an agreement with Tottenham for the transfer of Hugo Lloris.
"The proposals put forward this evening by Tottenham are very different from the principle which had been agreed on August 26, which had allowed to player to talk to the London club."
Spurs had been looking to sign a younger goalkeeper to provide competition for Brad Friedel, with manager Andre Villas-Boad admitting that Lloris was a target.
"We are very comfortable with out goalkeepers but there is a future to prepare for," Villas-Boas said.
"We have studied possibilities in that position and throughout the goalkeepers available, Hugo is one of the best."
Spurs and Lyon have until tomorrow's deadline to reach an agreement.