The German giants are undergoing a rebuild this summer as experienced stars Mats Hummels, Franck Ribery and Arjen Robben have all left the club.
Bayern have already splashed the cash on Lucas Hernandez (£68million) and Benjamin Pavard (£32m) but it has not stopped Neuer from raising doubts over his future.
Matthaus believes Neuer and his agent were wrong to publicly aim a dig at Bayern Munich as the captain could have spoken to the club’s top brass privately.
‘His behaviour is totally unacceptable,’ Matthaus told German newspaper Bild.
‘As the captain of Bayern he should speak to the club if he has a problem with the situation over signings.
‘The doors of the management are always open.’
Neuer’s agent Thomas Kroth previously said to Sueddeutsche Zeitung:
‘He is driven by success. My impression is that the gap between the top four English clubs is already serious, and Bayern, for the moment, is not sufficiently competitive to achieve Manuel’s objectives.
‘When he realises that Bayern are responding, then he will probably blossom again.
‘He does not want to retire in 2021. Now he is in the phase in which he has to decide: how will things progress in the future?
‘Signing a contract extension and ending his career at Bayern is of course the obvious option, but it’s not the only one.’
Neuer, who joined Bayern Munich from Schalke for £19.5m in 2011, has two more years left to run on his current deal at the Allianz Arena.
The 33-year-old has won seven Bundesliga titles, four German Cups and the Champions League during his successful spell in Munich.