Henze was seriously injured while returning in a taxi to the Olympic village early on Friday and has undergone emergency surgery, the team said.
"According to the doctors his head injuries are life-threatening," the DOSB said in a statement.
The 35-year-old Henze, a canoeing silver medallist at the Athens 2004 Olympics, was rushed to hospital. Another canoe team official, Christian Kaeding, suffered less serious injuries and was treated in hospital before being released.
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"After realising the extent of his injuries (Henze) was taken to a clinic with a special neurosurgical department and underwent emergency surgery," the DOSB said.
"The team around the leading Olympic doctor Bernd Wolfarth is in constant exchange with the doctors treating him."
Security and traffic have been major concerns for teams at the Rio Games while several official Olympic buses have been involved in traffic accidents.
Earlier on Friday a bus carrying journalists to one of the Olympic venues scraped another bus. No one was hurt in that incident.
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