Allardyce said, "It's a big disappointment because this is the second time we've failed to get Hamann," said the Trotters boss.
"I don't know why he's changed his mind - I haven't had an explanation.
Big Sam Misses Out On Hamann...........Again
"I would have liked Hamann because he could have done a job for us, but we haven't got him so we move on."
Hamann now looks set to join local rivals Manchester City.
Meanwhile, Middlesbrough boss Gareth Southgate will face competition from Bolton for the signing of pacey Lyon forward Sidney Govou.