The suspension of the 68-year-old, a special advisor to Fifa's Football Committee, comes after he refused repeated requests for assistance from Michael Garcia, the former US attorney who has led a two-year probe into corruption allegations on Fifa's behalf.
The particular offence is thought to relate to questions regarding the Qatar 2022 World Cup bid, with Beckenbauer having reportedly claimed that Garcia had "no power whatsoever" to demand his co-operation.
The case has now been passed on for formal investigation proceedings, with Vanessa Allard, the Ethics Committee's investigatory chamber member heading the panel which will decide whether Beckenbauer is open to further punishment.
A Fifa statement read: "Franz Beckenbauer was today provisionally banned from taking part in any football-related activity, at any level, for 90 days. The deputy chairman of the FIFA Ethics Committee’s adjudicatory chamber, Alan Sullivan, issued the ban at the request of the chairman of the investigatory chamber, Michael J. Garcia. The ban is effective immediately.
"The decision was taken pursuant to the FIFA Code of Ethics art. 83 par. 1, on the grounds that a breach of the Code of Ethics appears to have been committed and a decision on the main issue may not be taken early enough.
"The apparent breach relates to Mr Beckenbauer’s failure to cooperate with an Ethics Committee investigation despite repeated requests for his assistance, including requests that he provide information during an in-person interview or in response to written questions provided in both English and German."
Beckenbauer, who played 103 times for West Germany, won the 1972 European Championship and 1974 World Cup as a player before going on to coach his national side to the 1990 World Cup title.
He reacted with surprise to the news, telling Sky Sport Germany: “I had to check the date at first. I thought it was April the first and thus an April fool.”