The deal came as Toshiba's share price plunged nearly eight percent after a report it was under investigation by US authorities over allegations it hid losses in its nuclear business.
News of the Canon deal comes as Toshiba expects a whopping loss of about $6.0 billion for the year to March due to sagging global demand and a profit-padding scandal, in which high-handed bosses for years systematically pushed their subordinates to cover-up weak financial figures.
Under the deal Toshiba sold all its shares in Toshiba Medical Systems, a major producer of medical imaging tools such as MRI and CT scans, to Canon for 665.5 billion yen ($5.9 billion).
Separately, Toshiba said it had reached a basic accord to sell a majority interest in its home appliance business to China's Midea, though a Toshiba spokeswoman said a price for the deal had yet to be announced.
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In December, Japan's Securities and Exchange Surveillance Commission said Toshiba should be slapped with a record 7.37 billion yen fine over the profit-padding scheme that hammered the reputation of one of Japan's best-known firms.
Many Japanese high-tech companies are rushing to enter the medical field, as a greying population boosts demand for healthcare services and tools.
Sony launched a medical joint venture with endoscope maker Olympus, which also went through a massive loss-hiding scandal and required a strong partner to rebuild itself.
Bloomberg News, quoting unnamed sources, reported that the US Justice Department and the Securities and Exchange Commission are examining whether any fraud occurred.
Toshiba did not immediately respond to a request for comment on the report.