Bayern boss Heynckes confirmed on Wednesday that Neuer, 32, "won't play against Stuttgart [on Saturday]" but later suggested that the "decision for the cup final remains open."
The clash with Stuttgart is Bayern's final league game and, with the veteran boss unlikely to throw him in to the German Cup final against Frankfurt on May 19 without match practice, Heynckes' words mean that Neuer can, at best, only play in his country's two June friendlies before Germany kick off their World Cup defense against Mexico on June 17.
The former Schalke stopper admitted on Tuesday that ongoing problems with a fractured metatarsal mean his participation in Russia is in doubt.
Read more: The race to be Manuel Neuer's understudy
"I cannot say at the moment whether I will make the World Cup. I don't think it is conceivable that I can go into the World Cup without any match practice," he said.
Neuer, Germany's captain, said he remains in touch with national team boss Joachim Löw and goalkeeping coach Andreas Köpke and is working hard to build his fitness in order to give himself a chance. The World Cup winner returned to full training with Bayern three weeks ago but has yet to feature, despite the Bavarians having wrapped up the title early.
The 74-cap keeper has been a critical component of Löw's Germany side and Die Mannschaft general manager Oliver Bierhoff suggested he'd be given as much time as possible to prove his fitness.
"I’m still confident and convinced that Manuel will be at the World Cup," said Bierhoff. "We’re taking it day by day. For him – as is the case with other injured players – it’s important that they find their rhythm and concentrate in peace so that they return to fitness. The real deadline is June 4, when we have to nominate the final 23-man squad."
But former Bayern and Germany physio Oliver Schmidtlein told German publication Sport Bild that a comeback in the group stages of the World Cup - where Germany also play South Korea and Sweden - is impossible.
“I think the earliest he could play is in the knockout stages of the World Cup,” Schmidtlein said. "Manuel will not be able to train in this situation, despite the time pressure."
While Germany are relatively well-stocked in the goalkeeping department, with Barcelona keeper Marc-Andre ter Stegen the favorite to replace Neuer, Löw appears likely to take his skipper as part of his squad, even if he's not fit to start. Neuer's club deputy Sven Ulreich, Bayer Leverkusen's Bernd Leno and Kevin Trapp of Paris Saint-Germain are among the other options between the sticks.
Neuer is not the only injury worry for Löw. Jerome Boateng's participation is also in grave doubt, after he picked up a hamstring injury in Bayern's first leg Champions League loss to Real Madrid, while Arsenal's Mesut Özil will miss the rest of the club season with a back injury: "It'll need some time but I'm sure I'll fully recover in time for the World Cup," the playmaker wrote on Twitter.
Borussia Mönchengladbach's Lars Stindl has already been ruled out while Serge Gnabry, of Hoffenheim, is also in a race against time to prove his fitness.