Kroos' future was the subject of intense speculation during last month's transfer window, with Manchester United strongly linked with a move for the Germany international.
The 24-year-old's contract at the Allianz Arena is due to expire in 2015 and a number of clubs, including United, are thought to be monitoring his situation.
There have been suggestions that Kroos could be allowed to leave Bayern after a reported bust-up with manager Pep Guardiola.
However, Sammer insists everyone at Bayern wants to see Kroos remain at the Bundesliga giants for the long-term.
"We are aware that Toni Kroos is a very good player," Sammer told Sky Deutschland.
"We actually have a contract left to go with Toni Kroos and we clearly would want to keep on with him.
"Everyone at Bayern Munich is sharing this point of view."