United boss Ole Gunner Solskjaer claimed the midfielder would be in his squad for the New Year's Day trip to Arsenal.
But he was absent and Solskjaer revealed he now needs an ankle op that would keep him out for the whole of January.
Kroos came close to joining from Bayern Munich in the summer of 2014 but ended up at the Spanish giants.
If no such deal is agreed, Real will want Kroos, 29, to move somewhere else to make space for Pogba. United slapped a £180m price-tag on Pogba in the summer to scare of potential buyers.
But things have changed since then and he could now leave for £100m.